[bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

[bug#48575] [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

[zimoun]

Hi,

Janitor [1] patch set.  It moves Bioconductor packages from (gnu packages
bioinformatics) to (gnu packages bioconductor).

1: <https://lists.gnu.org/archive/html/guix-commits/2020-09/msg00416.html>


To transfer the Copyright, I use:

   git --no-pager log --date=format:"%Y" --format="%ad %an %s" --grep=r-<name>

I did my best to preserve the copyright.  But I do not guarantee it is error-free.
Well, in doubt, I have been conservative.

Then, I do:

   guix build r-<name> --no-grafts
   ./pre-inst-env guix build r-<name> --no-grafts --check

To avoid a break, I check with:

   for ci in $(git log --format="%H" -51 --reverse);
   do
      ./pre-inst-env guix pull --commit=$ci \
          -p /tmp/test-${ci} \
          --url=$(pwd) --branch=janitor --disable-authentication
   done

and everyting seems fine.  At least, "guix pull" should be checked at the end
of the series.


Last, I have checked the imported modules in gnu/packages/bioinformatics.scm.
All should be fine.

Now, I get:

--8<---------------cut here---------------start------------->8---
$ ag 'bioconductor' gnu/packages/bioinformatics.scm
69:  #:use-module (gnu packages bioconductor)
11550:      (synopsis "Extra base functions for Bioconductor")
11553:provided by Bioconductor packages.")
--8<---------------cut here---------------end--------------->8---

which ends the move, I guess.  Except the package r-rcurl in
gnu/packages/statistics.scm, let as an exercise for the reader. ;-)


On a side note about the Copyright lines, I did:

   git blame --date=format:"%Y)" gnu/packages/bioinformatics.scm \
     | cut -d')' -f1 | cut -d'(' -f2 | sed 's/ //g' \
     | sort | uniq -c

and it is possible that there is some "mistake", FWIW.

All the best,
simon


zimoun (50):
  gnu: r-genomicalignments: Move to (gnu packages bioconductor).
  gnu: r-rtracklayer: Move to (gnu packages bioconductor).
  gnu: r-genomicfeatures: Move to (gnu packages bioconductor).
  gnu: r-topgo: Move to (gnu packages bioconductor).
  gnu: r-bsgenome: Move to (gnu packages bioconductor).
  gnu: r-msnid: Move to (gnu packages bioconductor).
  gnu: r-msnbase: Move to (gnu packages bioconductor).
  gnu: r-samr: Move to (gnu packages bioconductor).
  gnu: r-impute: Move to (gnu packages bioconductor).
  gnu: r-seqpattern: Move to (gnu packages bioconductor).
  gnu: r-go-db: Move to (gnu packages bioconductor).
  gnu: r-genomation: Move to (gnu packages bioconductor).
  gnu: r-genomationdata: Move to (gnu packages bioconductor).
  gnu: r-pcamethods: Move to (gnu packages bioconductor).
  gnu: r-mzid: Move to (gnu packages bioconductor).
  gnu: r-aroma-light: Move to (gnu packages bioconductor).
  gnu: r-deseq: Move to (gnu packages bioconductor).
  gnu: r-edaseq: Move to (gnu packages bioconductor).
  gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).
  gnu: r-annotationhub: Move to (gnu packages bioconductor).
  gnu: r-fastseg: Move to (gnu packages bioconductor).
  gnu: r-affy: Move to (gnu packages bioconductor).
  gnu: r-keggrest: Move to (gnu packages bioconductor).
  gnu: r-gage: Move to (gnu packages bioconductor).
  gnu: r-complexheatmap: Move to (gnu packages bioconductor).
  gnu: r-genomicfiles: Move to (gnu packages bioconductor).
  gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).
  gnu: r-organismdbi: Move to (gnu packages bioconductor).
  gnu: r-affyio: Move to (gnu packages bioconductor).
  gnu: r-vsn: Move to (gnu packages bioconductor).
  gnu: r-biovizbase: Move to (gnu packages bioconductor).
  gnu: r-ensembldb: Move to (gnu packages bioconductor).
  gnu: r-mzr: Move to (gnu packages bioconductor).
  gnu: r-protgenerics: Move to (gnu packages bioconductor).
  gnu: r-sva: Move to (gnu packages bioconductor).
  gnu: r-motifrg: Move to (gnu packages bioconductor).
  gnu: r-seqlogo: Move to (gnu packages bioconductor).
  gnu: r-zlibbioc: Move to (gnu packages bioconductor).
  gnu: r-rhtslib: Move to (gnu packages bioconductor).
  gnu: r-bamsignals: Move to (gnu packages bioconductor).
  gnu: r-rcas: Move to (gnu packages bioconductor).
  gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).
  gnu: r-tximport: Move to (gnu packages bioconductor).
  gnu: r-rhdf5filters: Move to (gnu packages bioconductor).
  gnu: r-annotationfilter: Move to (gnu packages bioconductor).
  gnu: r-rhdf5: Move to (gnu packages bioconductor).
  gnu: r-chipseq: Move to (gnu packages bioconductor).
  gnu: r-copyhelper: Move to (gnu packages bioconductor).
  gnu: r-copywriter: Move to (gnu packages bioconductor).
  gnu: r-methylkit: Move to (gnu packages bioconductor).

 gnu/packages/bioconductor.scm   | 1826 +++++++++++++++++++++++++++++--
 gnu/packages/bioinformatics.scm | 1645 ----------------------------
 gnu/packages/cran.scm           |   30 -
 3 files changed, 1749 insertions(+), 1752 deletions(-)


base-commit: bd382fae71d899e243e81688bf5baed26171f2ea
-- 
2.30.1

[bug#48575] [PATCH 01/50] gnu: r-genomicalignments: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomicalignments): Move from here...
* gnu/packages/bioconductor.scm (r-genomicalignments): ...to here.
---
 gnu/packages/bioconductor.scm   | 35 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 33 -------------------------------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 45e31a5760..4f4ff82ad0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
+;;; Copyright © 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net>
 ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org>
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
@@ -2075,6 +2075,39 @@ translation between different chromosome sequence naming conventions (e.g.,
 names in their natural, rather than lexicographic, order.")
     (license license:artistic2.0)))
 
+(define-public r-genomicalignments
+  (package
+    (name "r-genomicalignments")
+    (version "1.26.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicAlignments" version))
+              (sha256
+               (base32
+                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
+    (properties
+     `((upstream-name . "GenomicAlignments")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (home-page "https://bioconductor.org/packages/GenomicAlignments")
+    (synopsis "Representation and manipulation of short genomic alignments")
+    (description
+     "This package provides efficient containers for storing and manipulating
+short genomic alignments (typically obtained by aligning short reads to a
+reference genome).  This includes read counting, computing the coverage,
+junction detection, and working with the nucleotide content of the
+alignments.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c77d66a35..0d0fe1df30 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,39 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomicalignments
-  (package
-    (name "r-genomicalignments")
-    (version "1.26.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicAlignments" version))
-              (sha256
-               (base32
-                "1q95px6s6snsax4ax955zzpdlrwp5liwf70wqq0lrk9mp6lq0hbr"))))
-    (properties
-     `((upstream-name . "GenomicAlignments")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)))
-    (home-page "https://bioconductor.org/packages/GenomicAlignments")
-    (synopsis "Representation and manipulation of short genomic alignments")
-    (description
-     "This package provides efficient containers for storing and manipulating
-short genomic alignments (typically obtained by aligning short reads to a
-reference genome).  This includes read counting, computing the coverage,
-junction detection, and working with the nucleotide content of the
-alignments.")
-    (license license:artistic2.0)))
-
 (define-public r-rtracklayer
   (package
     (name "r-rtracklayer")
-- 
2.30.1

[bug#48575] [PATCH 02/50] gnu: r-rtracklayer: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rtracklayer): Move from here...
* gnu/packages/bioconductor.scm (r-rtracklayer): ...to here.
---
 gnu/packages/bioconductor.scm   | 48 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 48 ---------------------------------
 2 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4f4ff82ad0..42a3d1fffc 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2385,6 +2385,54 @@ Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed
 tab-delimited (tabix) files.")
     (license license:expat)))
 
+(define-public r-rtracklayer
+  (package
+    (name "r-rtracklayer")
+    (version "1.50.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "rtracklayer" version))
+              (sha256
+               (base32
+                "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-zlib
+           (lambda _
+             (substitute* "DESCRIPTION"
+               ((" zlibbioc,") ""))
+             (substitute* "NAMESPACE"
+               (("import\\(zlibbioc\\)") ""))
+             #t)))))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xml" ,r-xml)
+       ("r-xvector" ,r-xvector)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (home-page "https://bioconductor.org/packages/rtracklayer")
+    (synopsis "R interface to genome browsers and their annotation tracks")
+    (description
+     "rtracklayer is an extensible framework for interacting with multiple
+genome browsers (currently UCSC built-in) and manipulating annotation tracks
+in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
+built-in).  The user may export/import tracks to/from the supported browsers,
+as well as query and modify the browser state, such as the current viewport.")
+    (license license:artistic2.0)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0d0fe1df30..9fb46c0d5d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-rtracklayer
-  (package
-    (name "r-rtracklayer")
-    (version "1.50.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "rtracklayer" version))
-              (sha256
-               (base32
-                "12zimhpdzjyzd81wrzz5hdbzvlgzcs22x1nnaf2jq4cba3ch5px8"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-zlib
-           (lambda _
-             (substitute* "DESCRIPTION"
-               ((" zlibbioc,") ""))
-             (substitute* "NAMESPACE"
-               (("import\\(zlibbioc\\)") ""))
-             #t)))))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xml" ,r-xml)
-       ("r-xvector" ,r-xvector)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (home-page "https://bioconductor.org/packages/rtracklayer")
-    (synopsis "R interface to genome browsers and their annotation tracks")
-    (description
-     "rtracklayer is an extensible framework for interacting with multiple
-genome browsers (currently UCSC built-in) and manipulating annotation tracks
-in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit
-built-in).  The user may export/import tracks to/from the supported browsers,
-as well as query and modify the browser state, such as the current viewport.")
-    (license license:artistic2.0)))
-
 (define-public r-genomicfeatures
   (package
     (name "r-genomicfeatures")
-- 
2.30.1

[bug#48575] [PATCH 03/50] gnu: r-genomicfeatures: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomicfeatures): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfeatures): ...to here.
---
 gnu/packages/bioconductor.scm   | 43 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 43 ---------------------------------
 2 files changed, 43 insertions(+), 43 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 42a3d1fffc..2263c17cc4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2108,6 +2108,49 @@ junction detection, and working with the nucleotide content of the
 alignments.")
     (license license:artistic2.0)))
 
+(define-public r-genomicfeatures
+  (package
+    (name "r-genomicfeatures")
+    (version "1.42.3")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GenomicFeatures" version))
+              (sha256
+               (base32
+                "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
+    (properties
+     `((upstream-name . "GenomicFeatures")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcurl" ,r-rcurl)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/GenomicFeatures")
+    (synopsis "Tools for working with transcript centric annotations")
+    (description
+     "This package provides a set of tools and methods for making and
+manipulating transcript centric annotations.  With these tools the user can
+easily download the genomic locations of the transcripts, exons and cds of a
+given organism, from either the UCSC Genome Browser or a BioMart
+database (more sources will be supported in the future).  This information is
+then stored in a local database that keeps track of the relationship between
+transcripts, exons, cds and genes.  Flexible methods are provided for
+extracting the desired features in a convenient format.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9fb46c0d5d..bf8cb2f3a5 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,49 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomicfeatures
-  (package
-    (name "r-genomicfeatures")
-    (version "1.42.3")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "GenomicFeatures" version))
-              (sha256
-               (base32
-                "168cf261vmcqffbzassavkjyz9a2af0l6zbv9cagkx6b1qrk3siz"))))
-    (properties
-     `((upstream-name . "GenomicFeatures")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcurl" ,r-rcurl)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/GenomicFeatures")
-    (synopsis "Tools for working with transcript centric annotations")
-    (description
-     "This package provides a set of tools and methods for making and
-manipulating transcript centric annotations.  With these tools the user can
-easily download the genomic locations of the transcripts, exons and cds of a
-given organism, from either the UCSC Genome Browser or a BioMart
-database (more sources will be supported in the future).  This information is
-then stored in a local database that keeps track of the relationship between
-transcripts, exons, cds and genes.  Flexible methods are provided for
-extracting the desired features in a convenient format.")
-    (license license:artistic2.0)))
-
 (define-public r-go-db
   (package
     (name "r-go-db")
-- 
2.30.1

[bug#48575] [PATCH 04/50] gnu: r-topgo: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-topgo): Move from here...
* gnu/packages/bioconductor.scm (r-topgo): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 33 ---------------------------------
 2 files changed, 33 insertions(+), 33 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2263c17cc4..2afb5214ee 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2607,6 +2607,39 @@ experimental designs is facilitated by a consistently implemented sample
 annotation infrastructure.")
     (license license:artistic2.0)))
 
+(define-public r-topgo
+  (package
+    (name "r-topgo")
+    (version "2.42.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "topGO" version))
+              (sha256
+               (base32
+                "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
+    (properties
+     `((upstream-name . "topGO")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-dbi" ,r-dbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-lattice" ,r-lattice)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-sparsem" ,r-sparsem)))
+    (home-page "https://bioconductor.org/packages/topGO")
+    (synopsis "Enrichment analysis for gene ontology")
+    (description
+     "The topGO package provides tools for testing @dfn{gene ontology} (GO)
+terms while accounting for the topology of the GO graph.  Different test
+statistics and different methods for eliminating local similarities and
+dependencies between GO terms can be implemented and applied.")
+    ;; Any version of the LGPL applies.
+    (license license:lgpl2.1+)))
+
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bf8cb2f3a5..32d2b6a683 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,39 +7873,6 @@ including VCF header and contents in RDF and JSON.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-topgo
-  (package
-    (name "r-topgo")
-    (version "2.42.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "topGO" version))
-              (sha256
-               (base32
-                "0vr3l9gvd3dhy446k3fkj6rm7z1abxi56rbnrs64297yzxaz1ngl"))))
-    (properties
-     `((upstream-name . "topGO")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-dbi" ,r-dbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-lattice" ,r-lattice)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-sparsem" ,r-sparsem)))
-    (home-page "https://bioconductor.org/packages/topGO")
-    (synopsis "Enrichment analysis for gene ontology")
-    (description
-     "The topGO package provides tools for testing @dfn{gene ontology} (GO)
-terms while accounting for the topology of the GO graph.  Different test
-statistics and different methods for eliminating local similarities and
-dependencies between GO terms can be implemented and applied.")
-    ;; Any version of the LGPL applies.
-    (license license:lgpl2.1+)))
-
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
-- 
2.30.1

[bug#48575] [PATCH 05/50] gnu: r-bsgenome: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-bsgenome): Move from here...
* gnu/packages/bioconductor.scm (r-bsgenome): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2afb5214ee..923413135b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
@@ -1875,6 +1875,37 @@ matching algorithms, and other utilities, for fast manipulation of large
 biological sequences or sets of sequences.")
     (license license:artistic2.0)))
 
+(define-public r-bsgenome
+  (package
+    (name "r-bsgenome")
+    (version "1.58.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BSgenome" version))
+              (sha256
+               (base32
+                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
+    (properties
+     `((upstream-name . "BSgenome")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/BSgenome")
+    (synopsis "Infrastructure for Biostrings-based genome data packages")
+    (description
+     "This package provides infrastructure shared by all Biostrings-based
+genome data packages and support for efficient SNP representation.")
+    (license license:artistic2.0)))
+
 (define-public r-category
   (package
     (name "r-category")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 32d2b6a683..9c9288c6b0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,37 +7873,6 @@ including VCF header and contents in RDF and JSON.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-bsgenome
-  (package
-    (name "r-bsgenome")
-    (version "1.58.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "BSgenome" version))
-              (sha256
-               (base32
-                "1gbvmxr6r57smgvhqgwspbcnwyk4hsfkxkpzzcs6470q03zfb4wq"))))
-    (properties
-     `((upstream-name . "BSgenome")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/BSgenome")
-    (synopsis "Infrastructure for Biostrings-based genome data packages")
-    (description
-     "This package provides infrastructure shared by all Biostrings-based
-genome data packages and support for efficient SNP representation.")
-    (license license:artistic2.0)))
-
 (define-public r-impute
   (package
     (name "r-impute")
-- 
2.30.1

[bug#48575] [PATCH 06/50] gnu: r-msnid: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-msnid): Move from here...
* gnu/packages/bioconductor.scm (r-msnid): ...to here.
---
 gnu/packages/bioconductor.scm   | 52 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 52 ---------------------------------
 2 files changed, 52 insertions(+), 52 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 923413135b..b5787cb207 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2312,6 +2312,58 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-msnid
+  (package
+    (name "r-msnid")
+    (version "1.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnID" version))
+       (sha256
+        (base32
+         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
+    (properties `((upstream-name . "MSnID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationhub" ,r-annotationhub)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocstyle" ,r-biocstyle)
+       ("r-biostrings" ,r-biostrings)
+       ("r-data-table" ,r-data-table)
+       ("r-doparallel" ,r-doparallel)
+       ("r-dplyr" ,r-dplyr)
+       ("r-foreach" ,r-foreach)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iterators" ,r-iterators)
+       ("r-msnbase" ,r-msnbase)
+       ("r-msmstests" ,r-msmstests)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-purrr" ,r-purrr)
+       ("r-r-cache" ,r-r-cache)
+       ("r-rcpp" ,r-rcpp)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rlang" ,r-rlang)
+       ("r-runit" ,r-runit)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-xtable" ,r-xtable)))
+    (home-page "https://bioconductor.org/packages/MSnID")
+    (synopsis "Utilities for LC-MSn proteomics identifications")
+    (description
+     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
+from mzIdentML (leveraging the mzID package) or text files.  After collating
+the search results from multiple datasets it assesses their identification
+quality and optimize filtering criteria to achieve the maximum number of
+identifications while not exceeding a specified false discovery rate.  It also
+contains a number of utilities to explore the MS/MS results and assess missed
+and irregular enzymatic cleavages, mass measurement accuracy, etc.")
+    (license license:artistic2.0)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9c9288c6b0..5c2abe6e94 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9275,58 +9275,6 @@ structure (pcaRes) to provide a common interface to the PCA results.")
 of mass spectrometry based proteomics data.")
     (license license:artistic2.0)))
 
-(define-public r-msnid
-  (package
-    (name "r-msnid")
-    (version "1.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MSnID" version))
-       (sha256
-        (base32
-         "05bncy7lw2a3h8xgnavjiz56pc6mk8q7l6qdd81197nawxs3j02d"))))
-    (properties `((upstream-name . "MSnID")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationhub" ,r-annotationhub)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocstyle" ,r-biocstyle)
-       ("r-biostrings" ,r-biostrings)
-       ("r-data-table" ,r-data-table)
-       ("r-doparallel" ,r-doparallel)
-       ("r-dplyr" ,r-dplyr)
-       ("r-foreach" ,r-foreach)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iterators" ,r-iterators)
-       ("r-msnbase" ,r-msnbase)
-       ("r-msmstests" ,r-msmstests)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-purrr" ,r-purrr)
-       ("r-r-cache" ,r-r-cache)
-       ("r-rcpp" ,r-rcpp)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rlang" ,r-rlang)
-       ("r-runit" ,r-runit)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-xtable" ,r-xtable)))
-    (home-page "https://bioconductor.org/packages/MSnID")
-    (synopsis "Utilities for LC-MSn proteomics identifications")
-    (description
-     "This package extracts @dfn{tandem mass spectrometry} (MS/MS) ID data
-from mzIdentML (leveraging the mzID package) or text files.  After collating
-the search results from multiple datasets it assesses their identification
-quality and optimize filtering criteria to achieve the maximum number of
-identifications while not exceeding a specified false discovery rate.  It also
-contains a number of utilities to explore the MS/MS results and assess missed
-and irregular enzymatic cleavages, mass measurement accuracy, etc.")
-    (license license:artistic2.0)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-- 
2.30.1

[bug#48575] [PATCH 07/50] gnu: r-msnbase: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-msnbase): Move from here...
* gnu/packages/bioconductor.scm (r-msnbase): ...to here.
---
 gnu/packages/bioconductor.scm   | 45 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 45 ---------------------------------
 2 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b5787cb207..58c8336ce5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2312,6 +2312,51 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-msnbase
+  (package
+    (name "r-msnbase")
+    (version "2.16.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MSnbase" version))
+       (sha256
+        (base32
+         "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))
+    (properties `((upstream-name . "MSnbase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-digest" ,r-digest)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-impute" ,r-impute)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-maldiquant" ,r-maldiquant)
+       ("r-mass" ,r-mass)
+       ("r-mzid" ,r-mzid)
+       ("r-mzr" ,r-mzr)
+       ("r-pcamethods" ,r-pcamethods)
+       ("r-plyr" ,r-plyr)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-vsn" ,r-vsn)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/lgatto/MSnbase")
+    (synopsis "Base functions and classes for MS-based proteomics")
+    (description
+     "This package provides basic plotting, data manipulation and processing
+of mass spectrometry based proteomics data.")
+    (license license:artistic2.0)))
+
 (define-public r-msnid
   (package
     (name "r-msnid")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5c2abe6e94..28893c40e7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9230,51 +9230,6 @@ the results is also provided.  All PCA methods make use of the same data
 structure (pcaRes) to provide a common interface to the PCA results.")
     (license license:gpl3+)))
 
-(define-public r-msnbase
-  (package
-    (name "r-msnbase")
-    (version "2.16.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MSnbase" version))
-       (sha256
-        (base32
-         "0hxzs9zzljywqxr7q388hshpy1pdryhl0zkwffqbxpf5pcf92d3h"))))
-    (properties `((upstream-name . "MSnbase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-digest" ,r-digest)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-maldiquant" ,r-maldiquant)
-       ("r-mass" ,r-mass)
-       ("r-mzid" ,r-mzid)
-       ("r-mzr" ,r-mzr)
-       ("r-pcamethods" ,r-pcamethods)
-       ("r-plyr" ,r-plyr)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-vsn" ,r-vsn)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/lgatto/MSnbase")
-    (synopsis "Base functions and classes for MS-based proteomics")
-    (description
-     "This package provides basic plotting, data manipulation and processing
-of mass spectrometry based proteomics data.")
-    (license license:artistic2.0)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-- 
2.30.1

[bug#48575] [PATCH 08/50] gnu: r-samr: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/cran.scm (r-samr): Move from here...
* gnu/packages/bioconductor.scm (r-samr): ...to here.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 gnu/packages/cran.scm         | 30 ------------------------------
 2 files changed, 31 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 58c8336ce5..f9aa34d254 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -10,6 +10,7 @@
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
+;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -2604,6 +2605,36 @@ built-in).  The user may export/import tracks to/from the supported browsers,
 as well as query and modify the browser state, such as the current viewport.")
     (license license:artistic2.0)))
 
+;; This is a CRAN package, but it depends on a Bioconductor package.
+(define-public r-samr
+  (package
+    (name "r-samr")
+    (version "3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "samr" version))
+       (sha256
+        (base32
+         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
+    (properties `((upstream-name . "samr")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-gsa" ,r-gsa)
+       ("r-impute" ,r-impute)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-openxlsx" ,r-openxlsx)
+       ("r-shiny" ,r-shiny)
+       ("r-shinyfiles" ,r-shinyfiles)))
+    (native-inputs `(("gfortran" ,gfortran)))
+    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
+    (synopsis "Significance analysis of Microarrays")
+    (description
+     "This is a package for significance analysis of Microarrays for
+differential expression analysis, RNAseq data and related problems.")
+    ;; Any version of the LGPL
+    (license license:lgpl3+)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 8709cd21fa..e5d1db7cb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -33,7 +33,6 @@
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
 ;;; Copyright © 2020 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
-;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -28629,35 +28628,6 @@ indicator, a quantitative variable or a survival time.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
-(define-public r-samr
-  (package
-    (name "r-samr")
-    (version "3.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (cran-uri "samr" version))
-       (sha256
-        (base32
-         "01km0f7qgm73x19vbvsxl083hs1dq4dj8qm5h64cxbf20b08my15"))))
-    (properties `((upstream-name . "samr")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-gsa" ,r-gsa)
-       ("r-impute" ,r-impute)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-openxlsx" ,r-openxlsx)
-       ("r-shiny" ,r-shiny)
-       ("r-shinyfiles" ,r-shinyfiles)))
-    (native-inputs `(("gfortran" ,gfortran)))
-    (home-page "https://statweb.stanford.edu/~tibs/SAM/")
-    (synopsis "Significance analysis of Microarrays")
-    (description
-     "This is a package for significance analysis of Microarrays for
-differential expression analysis, RNAseq data and related problems.")
-    ;; Any version of the LGPL
-    (license license:lgpl3+)))
-
 (define-public r-randomforestsrc
   (package
     (name "r-randomforestsrc")
-- 
2.30.1

[bug#48575] [PATCH 09/50] gnu: r-impute: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-impute): Move from here...
* gnu/packages/bioconductor.scm (r-impute): ...to here.
---
 gnu/packages/bioconductor.scm   | 20 ++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 20 --------------------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f9aa34d254..0b40d70397 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2294,6 +2294,26 @@ Enrichment Analysis} (GSEA).")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-impute
+  (package
+    (name "r-impute")
+    (version "1.64.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "impute" version))
+              (sha256
+               (base32
+                "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
+    (native-inputs
+     `(("gfortran" ,gfortran)))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/impute")
+    (synopsis "Imputation for microarray data")
+    (description
+     "This package provides a function to impute missing gene expression
+microarray data, using nearest neighbor averaging.")
+    (license license:gpl2+)))
+
 (define-public r-limma
   (package
     (name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 28893c40e7..ef5c1a3323 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,26 +7873,6 @@ including VCF header and contents in RDF and JSON.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-impute
-  (package
-    (name "r-impute")
-    (version "1.64.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "impute" version))
-              (sha256
-               (base32
-                "1pnjasw9i19nmxwjzrd9jbln31yc5jilfvwk414ya5zbqfsazvxa"))))
-    (native-inputs
-     `(("gfortran" ,gfortran)))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/impute")
-    (synopsis "Imputation for microarray data")
-    (description
-     "This package provides a function to impute missing gene expression
-microarray data, using nearest neighbor averaging.")
-    (license license:gpl2+)))
-
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
-- 
2.30.1

[bug#48575] [PATCH 10/50] gnu: r-seqpattern: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-seqpattern): Move from here...
* gnu/packages/bioconductor.scm (r-seqpattern): ...to here.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0b40d70397..1b1b00cde0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2655,6 +2655,33 @@ differential expression analysis, RNAseq data and related problems.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
+(define-public r-seqpattern
+  (package
+    (name "r-seqpattern")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "seqPattern" version))
+              (sha256
+               (base32
+                "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
+    (properties
+     `((upstream-name . "seqPattern")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-plotrix" ,r-plotrix)))
+    (home-page "https://bioconductor.org/packages/seqPattern")
+    (synopsis "Visualising oligonucleotide patterns and motif occurrences")
+    (description
+     "This package provides tools to visualize oligonucleotide patterns and
+sequence motif occurrences across a large set of sequences centred at a common
+reference point and sorted by a user defined feature.")
+    (license license:gpl3+)))
+
 (define-public r-shortread
   (package
     (name "r-shortread")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef5c1a3323..71e1481af2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7873,33 +7873,6 @@ including VCF header and contents in RDF and JSON.")
 information about the latest version of the Gene Ontologies.")
     (license license:artistic2.0)))
 
-(define-public r-seqpattern
-  (package
-    (name "r-seqpattern")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "seqPattern" version))
-              (sha256
-               (base32
-                "0j68n6fwycxjpl2va5fw7ajb123n758s2pq997d76dysxghmrlzq"))))
-    (properties
-     `((upstream-name . "seqPattern")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-plotrix" ,r-plotrix)))
-    (home-page "https://bioconductor.org/packages/seqPattern")
-    (synopsis "Visualising oligonucleotide patterns and motif occurrences")
-    (description
-     "This package provides tools to visualize oligonucleotide patterns and
-sequence motif occurrences across a large set of sequences centred at a common
-reference point and sorted by a user defined feature.")
-    (license license:gpl3+)))
-
 (define-public r-genomation
   (package
     (name "r-genomation")
-- 
2.30.1

[bug#48575] [PATCH 11/50] gnu: r-go-db: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-go-db): Move from here...
* gnu/packages/bioconductor.scm (r-go-db): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'annotation.
---
 gnu/packages/bioconductor.scm   | 22 ++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 24 ------------------------
 2 files changed, 22 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1b1b00cde0..eb73909723 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -413,6 +413,28 @@ in Biostrings objects.")
 ID and species.  It is used by functions in the GenomeInfoDb package.")
     (license license:artistic2.0)))
 
+(define-public r-go-db
+  (package
+    (name "r-go-db")
+    (version "3.7.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "GO.db" version 'annotation))
+              (sha256
+               (base32
+                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
+    (properties
+     `((upstream-name . "GO.db")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)))
+    (home-page "https://bioconductor.org/packages/GO.db")
+    (synopsis "Annotation maps describing the entire Gene Ontology")
+    (description
+     "The purpose of this GO.db annotation package is to provide detailed
+information about the latest version of the Gene Ontologies.")
+    (license license:artistic2.0)))
+
 (define-public r-homo-sapiens
   (package
     (name "r-homo-sapiens")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71e1481af2..71f07748b6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,30 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-go-db
-  (package
-    (name "r-go-db")
-    (version "3.7.0")
-    (source (origin
-              (method url-fetch)
-              (uri (string-append "https://www.bioconductor.org/packages/"
-                                  "release/data/annotation/src/contrib/GO.db_"
-                                  version ".tar.gz"))
-              (sha256
-               (base32
-                "0i3wcf5h3n0dawzc1hy0kv74f06j80c47n4p3g3fmrcxlhi3jpa5"))))
-    (properties
-     `((upstream-name . "GO.db")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)))
-    (home-page "https://bioconductor.org/packages/GO.db")
-    (synopsis "Annotation maps describing the entire Gene Ontology")
-    (description
-     "The purpose of this GO.db annotation package is to provide detailed
-information about the latest version of the Gene Ontologies.")
-    (license license:artistic2.0)))
-
 (define-public r-genomation
   (package
     (name "r-genomation")
-- 
2.30.1

[bug#48575] [PATCH 12/50] gnu: r-genomation: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomation): Move from here...
* gnu/packages/bioconductor.scm (r-genomation): ...to here.
---
 gnu/packages/bioconductor.scm   | 48 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 48 ---------------------------------
 2 files changed, 48 insertions(+), 48 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eb73909723..2be7920770 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2099,6 +2099,54 @@ CAGE.")
 high-throughput sequencing experiments.")
     (license license:artistic2.0)))
 
+(define-public r-genomation
+  (package
+    (name "r-genomation")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "genomation" version))
+              (sha256
+               (base32
+                "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-data-table" ,r-data-table)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gridbase" ,r-gridbase)
+       ("r-impute" ,r-impute)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-plotrix" ,r-plotrix)
+       ("r-plyr" ,r-plyr)
+       ("r-rcpp" ,r-rcpp)
+       ("r-readr" ,r-readr)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-runit" ,r-runit)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-seqpattern" ,r-seqpattern)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+    (synopsis "Summary, annotation and visualization of genomic data")
+    (description
+     "This package provides a package for summary and annotation of genomic
+intervals.  Users can visualize and quantify genomic intervals over
+pre-defined functional regions, such as promoters, exons, introns, etc.  The
+genomic intervals represent regions with a defined chromosome position, which
+may be associated with a score, such as aligned reads from HT-seq experiments,
+TF binding sites, methylation scores, etc.  The package can use any tabular
+genomic feature data as long as it has minimal information on the locations of
+genomic intervals.  In addition, it can use BAM or BigWig files as input.")
+    (license license:artistic2.0)))
+
 (define-public r-genomeinfodb
   (package
     (name "r-genomeinfodb")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71f07748b6..f8e7b2cab9 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,54 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomation
-  (package
-    (name "r-genomation")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "genomation" version))
-              (sha256
-               (base32
-                "1ana06irlpdgnmk8mb329nws9sm8n6max4qargf1xdcdf3rnk45g"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-data-table" ,r-data-table)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-gridbase" ,r-gridbase)
-       ("r-impute" ,r-impute)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-plotrix" ,r-plotrix)
-       ("r-plyr" ,r-plyr)
-       ("r-rcpp" ,r-rcpp)
-       ("r-readr" ,r-readr)
-       ("r-reshape2" ,r-reshape2)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-runit" ,r-runit)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-seqpattern" ,r-seqpattern)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
-    (synopsis "Summary, annotation and visualization of genomic data")
-    (description
-     "This package provides a package for summary and annotation of genomic
-intervals.  Users can visualize and quantify genomic intervals over
-pre-defined functional regions, such as promoters, exons, introns, etc.  The
-genomic intervals represent regions with a defined chromosome position, which
-may be associated with a score, such as aligned reads from HT-seq experiments,
-TF binding sites, methylation scores, etc.  The package can use any tabular
-genomic feature data as long as it has minimal information on the locations of
-genomic intervals.  In addition, it can use BAM or BigWig files as input.")
-    (license license:artistic2.0)))
-
 (define-public r-genomationdata
   (package
     (name "r-genomationdata")
-- 
2.30.1

[bug#48575] [PATCH 13/50] gnu: r-genomationdata: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomationdata): Move from here...
* gnu/packages/bioconductor.scm (r-genomationdata): ...to here.
[source]: Replace 'string-append' by 'bioconductor-uri' with 'experiment.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 2 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2be7920770..22b5a6068e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1021,6 +1021,32 @@ chromstaR package.")
 genomes and gene ID formats, largely based on the UCSC table browser.")
     (license license:lgpl2.0+)))
 
+(define-public r-genomationdata
+  (package
+    (name "r-genomationdata")
+    (version "1.22.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "genomationData" version 'experiment))
+              (sha256
+               (base32
+                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
+    (properties
+     `((upstream-name . "genomationData")))
+    (build-system r-build-system)
+    ;; As this package provides little more than large data files, it doesn't
+    ;; make sense to build substitutes.
+    (arguments `(#:substitutable? #f))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
+    (synopsis "Experimental data for use with the genomation package")
+    (description
+     "This package contains experimental genetic data for use with the
+genomation package.  Included are Chip Seq, Methylation and Cage data,
+downloaded from Encode.")
+    (license license:gpl3+)))
+
 (define-public r-pasilla
   (package
     (name "r-pasilla")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f8e7b2cab9..87254a9058 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,34 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-genomationdata
-  (package
-    (name "r-genomationdata")
-    (version "1.22.0")
-    (source (origin
-              (method url-fetch)
-              ;; We cannot use bioconductor-uri here because this tarball is
-              ;; located under "data/annotation/" instead of "bioc/".
-              (uri (string-append "https://bioconductor.org/packages/"
-                                  "release/data/experiment/src/contrib/"
-                                  "genomationData_" version ".tar.gz"))
-              (sha256
-               (base32
-                "0igjsvfnws3498j65ifniw0kbxfqpfr59rcjddqvq4zsj453fx1g"))))
-    (build-system r-build-system)
-    ;; As this package provides little more than large data files, it doesn't
-    ;; make sense to build substitutes.
-    (arguments `(#:substitutable? #f))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioinformatics.mdc-berlin.de/genomation/")
-    (synopsis "Experimental data for use with the genomation package")
-    (description
-     "This package contains experimental genetic data for use with the
-genomation package.  Included are Chip Seq, Methylation and Cage data,
-downloaded from Encode.")
-    (license license:gpl3+)))
-
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")
-- 
2.30.1

[bug#48575] [PATCH 14/50] gnu: r-pcamethods: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-pcamethods): Move from here...
* gnu/packages/bioconductor.scm (r-pcamethods): ...to here.
---
 gnu/packages/bioconductor.scm   | 30 ++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 30 ------------------------------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 22b5a6068e..1533e5b8f9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2526,6 +2526,36 @@ contains a number of utilities to explore the MS/MS results and assess missed
 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
+(define-public r-pcamethods
+  (package
+    (name "r-pcamethods")
+    (version "1.82.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "pcaMethods" version))
+       (sha256
+        (base32
+         "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
+    (properties `((upstream-name . "pcaMethods")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-mass" ,r-mass)
+       ("r-rcpp" ,r-rcpp)))
+    (home-page "https://github.com/hredestig/pcamethods")
+    (synopsis "Collection of PCA methods")
+    (description
+     "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
+Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
+for missing value estimation is included for comparison.  BPCA, PPCA and
+NipalsPCA may be used to perform PCA on incomplete data as well as for
+accurate missing value estimation.  A set of methods for printing and plotting
+the results is also provided.  All PCA methods make use of the same data
+structure (pcaRes) to provide a common interface to the PCA results.")
+    (license license:gpl3+)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 87254a9058..a98f3d5d8a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9053,36 +9053,6 @@ mzIdentML files with the drawback of having less pretty output than a vendor
 specific parser.")
     (license license:gpl2+)))
 
-(define-public r-pcamethods
-  (package
-    (name "r-pcamethods")
-    (version "1.82.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "pcaMethods" version))
-       (sha256
-        (base32
-         "04xb4vjky6hq58l30i1iq9rv5gzjdxnidjxpnzg7pvg67vz8pgf0"))))
-    (properties `((upstream-name . "pcaMethods")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-mass" ,r-mass)
-       ("r-rcpp" ,r-rcpp)))
-    (home-page "https://github.com/hredestig/pcamethods")
-    (synopsis "Collection of PCA methods")
-    (description
-     "This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA,
-Inverse Non-Linear PCA and the conventional SVD PCA.  A cluster based method
-for missing value estimation is included for comparison.  BPCA, PPCA and
-NipalsPCA may be used to perform PCA on incomplete data as well as for
-accurate missing value estimation.  A set of methods for printing and plotting
-the results is also provided.  All PCA methods make use of the same data
-structure (pcaRes) to provide a common interface to the PCA results.")
-    (license license:gpl3+)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-- 
2.30.1

[bug#48575] [PATCH 15/50] gnu: r-mzid: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-mzid): Move from here...
* gnu/packages/bioconductor.scm (r-mzid): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1533e5b8f9..5e0b722e2f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2526,6 +2526,37 @@ contains a number of utilities to explore the MS/MS results and assess missed
 and irregular enzymatic cleavages, mass measurement accuracy, etc.")
     (license license:artistic2.0)))
 
+(define-public r-mzid
+  (package
+    (name "r-mzid")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzID" version))
+       (sha256
+        (base32
+         "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
+    (properties `((upstream-name . "mzID")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-doparallel" ,r-doparallel)
+       ("r-foreach" ,r-foreach)
+       ("r-iterators" ,r-iterators)
+       ("r-plyr" ,r-plyr)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-xml" ,r-xml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/mzID")
+    (synopsis "Parser for mzIdentML files")
+    (description
+     "This package provides a parser for mzIdentML files implemented using the
+XML package.  The parser tries to be general and able to handle all types of
+mzIdentML files with the drawback of having less pretty output than a vendor
+specific parser.")
+    (license license:gpl2+)))
+
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a98f3d5d8a..5b6426e17d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-mzid
-  (package
-    (name "r-mzid")
-    (version "1.28.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "mzID" version))
-       (sha256
-        (base32
-         "0s7d6cz1li7v3ni6n6hrdspl93yiyr283kmbbd3hhkfgzgx6kpq2"))))
-    (properties `((upstream-name . "mzID")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-doparallel" ,r-doparallel)
-       ("r-foreach" ,r-foreach)
-       ("r-iterators" ,r-iterators)
-       ("r-plyr" ,r-plyr)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-xml" ,r-xml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/mzID")
-    (synopsis "Parser for mzIdentML files")
-    (description
-     "This package provides a parser for mzIdentML files implemented using the
-XML package.  The parser tries to be general and able to handle all types of
-mzIdentML files with the drawback of having less pretty output than a vendor
-specific parser.")
-    (license license:gpl2+)))
-
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
-- 
2.30.1

[bug#48575] [PATCH 16/50] gnu: r-aroma-light: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-aroma-light): Move from here...
* gnu/packages/bioconductor.scm (r-aroma-light): ...to here.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5e0b722e2f..e58cd66fef 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1782,6 +1782,33 @@ annotation data packages using SQLite data storage.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-aroma-light
+  (package
+    (name "r-aroma-light")
+    (version "3.20.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "aroma.light" version))
+       (sha256
+        (base32
+         "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
+    (properties `((upstream-name . "aroma.light")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-matrixstats" ,r-matrixstats)
+       ("r-r-methodss3" ,r-r-methodss3)
+       ("r-r-oo" ,r-r-oo)
+       ("r-r-utils" ,r-r-utils)))
+    (home-page "https://github.com/HenrikBengtsson/aroma.light")
+    (synopsis "Methods for normalization and visualization of microarray data")
+    (description
+     "This package provides methods for microarray analysis that take basic
+data types such as matrices and lists of vectors.  These methods can be used
+standalone, be utilized in other packages, or be wrapped up in higher-level
+classes.")
+    (license license:gpl2+)))
+
 (define-public r-biobase
   (package
     (name "r-biobase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5b6426e17d..c8444eea9f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-aroma-light
-  (package
-    (name "r-aroma-light")
-    (version "3.20.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "aroma.light" version))
-       (sha256
-        (base32
-         "0pi37rlfqh24p9wd7l1xb3f7c7938xdscgcc5agp8c9qhajq25a0"))))
-    (properties `((upstream-name . "aroma.light")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-matrixstats" ,r-matrixstats)
-       ("r-r-methodss3" ,r-r-methodss3)
-       ("r-r-oo" ,r-r-oo)
-       ("r-r-utils" ,r-r-utils)))
-    (home-page "https://github.com/HenrikBengtsson/aroma.light")
-    (synopsis "Methods for normalization and visualization of microarray data")
-    (description
-     "This package provides methods for microarray analysis that take basic
-data types such as matrices and lists of vectors.  These methods can be used
-standalone, be utilized in other packages, or be wrapped up in higher-level
-classes.")
-    (license license:gpl2+)))
-
 (define-public r-deseq
   (package
     (name "r-deseq")
-- 
2.30.1

[bug#48575] [PATCH 17/50] gnu: r-deseq: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-deseq): Move from here...
* gnu/packages/bioconductor.scm (r-deseq): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e58cd66fef..69ef513bc6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2013,6 +2013,37 @@ genome data packages and support for efficient SNP representation.")
 analysis.")
     (license license:artistic2.0)))
 
+(define-public r-deseq
+  (package
+    (name "r-deseq")
+    (version "1.39.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DESeq" version))
+       (sha256
+        (base32
+         "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
+    (properties `((upstream-name . "DESeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genefilter" ,r-genefilter)
+       ("r-geneplotter" ,r-geneplotter)
+       ("r-lattice" ,r-lattice)
+       ("r-locfit" ,r-locfit)
+       ("r-mass" ,r-mass)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)))
+    (home-page "https://www-huber.embl.de/users/anders/DESeq/")
+    (synopsis "Differential gene expression analysis")
+    (description
+     "This package provides tools for estimating variance-mean dependence in
+count data from high-throughput genetic sequencing assays and for testing for
+differential expression based on a model using the negative binomial
+distribution.")
+    (license license:gpl3+)))
+
 (define-public r-deseq2
   (package
     (name "r-deseq2")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c8444eea9f..2edb501f9b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,37 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-deseq
-  (package
-    (name "r-deseq")
-    (version "1.39.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DESeq" version))
-       (sha256
-        (base32
-         "047hph5aqmjnz1aqprziw0smdn5lf96hmwpnvqrxv1j2yfvcf3h1"))))
-    (properties `((upstream-name . "DESeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genefilter" ,r-genefilter)
-       ("r-geneplotter" ,r-geneplotter)
-       ("r-lattice" ,r-lattice)
-       ("r-locfit" ,r-locfit)
-       ("r-mass" ,r-mass)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)))
-    (home-page "https://www-huber.embl.de/users/anders/DESeq/")
-    (synopsis "Differential gene expression analysis")
-    (description
-     "This package provides tools for estimating variance-mean dependence in
-count data from high-throughput genetic sequencing assays and for testing for
-differential expression based on a model using the negative binomial
-distribution.")
-    (license license:gpl3+)))
-
 (define-public r-edaseq
   (package
     (name "r-edaseq")
-- 
2.30.1

[bug#48575] [PATCH 18/50] gnu: r-edaseq: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-edaseq): Move from here...
* gnu/packages/bioconductor.scm (r-edaseq): ...to here.
---
 gnu/packages/bioconductor.scm   | 40 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 40 ---------------------------------
 2 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 69ef513bc6..beb662984d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2127,6 +2127,46 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-edaseq
+  (package
+    (name "r-edaseq")
+    (version "2.24.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "EDASeq" version))
+       (sha256
+        (base32
+         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
+    (properties `((upstream-name . "EDASeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-aroma-light" ,r-aroma-light)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biomart" ,r-biomart)
+       ("r-biostrings" ,r-biostrings)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-shortread" ,r-shortread)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/drisso/EDASeq")
+    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
+    (description
+     "This package provides support for numerical and graphical summaries of
+RNA-Seq genomic read data.  Provided within-lane normalization procedures to
+adjust for GC-content effect (or other gene-level effects) on read counts:
+loess robust local regression, global-scaling, and full-quantile
+normalization.  Between-lane normalization procedures to adjust for
+distributional differences between lanes (e.g., sequencing depth):
+global-scaling and full-quantile normalization.")
+    (license license:artistic2.0)))
+
 (define-public r-edger
   (package
     (name "r-edger")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2edb501f9b..b0de0d9880 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,46 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-edaseq
-  (package
-    (name "r-edaseq")
-    (version "2.24.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "EDASeq" version))
-       (sha256
-        (base32
-         "0fznj7lsgkss1svv4rq8g87s1gmnbd7hccim41dv1c2w2nl0n2ip"))))
-    (properties `((upstream-name . "EDASeq")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-aroma-light" ,r-aroma-light)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biomart" ,r-biomart)
-       ("r-biostrings" ,r-biostrings)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-shortread" ,r-shortread)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/drisso/EDASeq")
-    (synopsis "Exploratory data analysis and normalization for RNA-Seq")
-    (description
-     "This package provides support for numerical and graphical summaries of
-RNA-Seq genomic read data.  Provided within-lane normalization procedures to
-adjust for GC-content effect (or other gene-level effects) on read counts:
-loess robust local regression, global-scaling, and full-quantile
-normalization.  Between-lane normalization procedures to adjust for
-distributional differences between lanes (e.g., sequencing depth):
-global-scaling and full-quantile normalization.")
-    (license license:artistic2.0)))
-
 (define-public r-interactivedisplaybase
   (package
     (name "r-interactivedisplaybase")
-- 
2.30.1

[bug#48575] [PATCH 19/50] gnu: r-interactivedisplaybase: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-interactivedisplaybase): Move from here...
* gnu/packages/bioconductor.scm (r-interactivedisplaybase): ...to here.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index beb662984d..9619ce5464 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2508,6 +2508,33 @@ the Human Protein Atlas project.")
 microarray data, using nearest neighbor averaging.")
     (license license:gpl2+)))
 
+(define-public r-interactivedisplaybase
+  (package
+    (name "r-interactivedisplaybase")
+    (version "1.28.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "interactiveDisplayBase" version))
+       (sha256
+        (base32
+         "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
+    (properties
+     `((upstream-name . "interactiveDisplayBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-dt" ,r-dt)
+       ("r-shiny" ,r-shiny)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
+    (synopsis "Base package for web displays of Bioconductor objects")
+    (description
+     "This package contains the basic methods needed to generate interactive
+Shiny-based display methods for Bioconductor objects.")
+    (license license:artistic2.0)))
+
 (define-public r-limma
   (package
     (name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b0de0d9880..b367dcae98 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,33 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-interactivedisplaybase
-  (package
-    (name "r-interactivedisplaybase")
-    (version "1.28.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "interactiveDisplayBase" version))
-       (sha256
-        (base32
-         "08id2hkx4ssxj34dildx00a4j3z0nv171b7b0wl6xjks7wk6lv01"))))
-    (properties
-     `((upstream-name . "interactiveDisplayBase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-dt" ,r-dt)
-       ("r-shiny" ,r-shiny)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/interactiveDisplayBase")
-    (synopsis "Base package for web displays of Bioconductor objects")
-    (description
-     "This package contains the basic methods needed to generate interactive
-Shiny-based display methods for Bioconductor objects.")
-    (license license:artistic2.0)))
-
 (define-public r-annotationhub
   (package
     (name "r-annotationhub")
-- 
2.30.1

[bug#48575] [PATCH 20/50] gnu: r-annotationhub: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-annotationhub): Move from here...
* gnu/packages/bioconductor.scm (r-annotationhub): ...to here.
---
 gnu/packages/bioconductor.scm   | 41 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 41 ---------------------------------
 2 files changed, 41 insertions(+), 41 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 9619ce5464..4657b0fa8b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1782,6 +1782,47 @@ annotation data packages using SQLite data storage.")
 databases.  Packages produced are intended to be used with AnnotationDbi.")
     (license license:artistic2.0)))
 
+(define-public r-annotationhub
+  (package
+    (name "r-annotationhub")
+    (version "2.22.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "AnnotationHub" version))
+       (sha256
+        (base32
+         "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
+    (properties `((upstream-name . "AnnotationHub")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biocfilecache" ,r-biocfilecache)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-biocversion" ,r-biocversion)
+       ("r-curl" ,r-curl)
+       ("r-dplyr" ,r-dplyr)
+       ("r-httr" ,r-httr)
+       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
+       ("r-rappdirs" ,r-rappdirs)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-yaml" ,r-yaml)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/AnnotationHub")
+    (synopsis "Client to access AnnotationHub resources")
+    (description
+     "This package provides a client for the Bioconductor AnnotationHub web
+resource.  The AnnotationHub web resource provides a central location where
+genomic files (e.g. VCF, bed, wig) and other resources from standard
+locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
+metadata about each resource, e.g., a textual description, tags, and date of
+modification.  The client creates and manages a local cache of files retrieved
+by the user, helping with quick and reproducible access.")
+    (license license:artistic2.0)))
+
 (define-public r-aroma-light
   (package
     (name "r-aroma-light")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b367dcae98..1dc2d6f977 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,47 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-annotationhub
-  (package
-    (name "r-annotationhub")
-    (version "2.22.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "AnnotationHub" version))
-       (sha256
-        (base32
-         "08d7m0n4jkpajsj0bvi5xd4vi1zqczl6lnrh8kqi2fbjkrvwdqp5"))))
-    (properties `((upstream-name . "AnnotationHub")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biocfilecache" ,r-biocfilecache)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-biocversion" ,r-biocversion)
-       ("r-curl" ,r-curl)
-       ("r-dplyr" ,r-dplyr)
-       ("r-httr" ,r-httr)
-       ("r-interactivedisplaybase" ,r-interactivedisplaybase)
-       ("r-rappdirs" ,r-rappdirs)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-yaml" ,r-yaml)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/AnnotationHub")
-    (synopsis "Client to access AnnotationHub resources")
-    (description
-     "This package provides a client for the Bioconductor AnnotationHub web
-resource.  The AnnotationHub web resource provides a central location where
-genomic files (e.g. VCF, bed, wig) and other resources from standard
-locations (e.g. UCSC, Ensembl) can be discovered.  The resource includes
-metadata about each resource, e.g., a textual description, tags, and date of
-modification.  The client creates and manages a local cache of files retrieved
-by the user, helping with quick and reproducible access.")
-    (license license:artistic2.0)))
-
 (define-public r-fastseg
   (package
     (name "r-fastseg")
-- 
2.30.1

[bug#48575] [PATCH 21/50] gnu: r-fastseg: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-fastseg): Move from here...
* gnu/packages/bioconductor.scm (r-fastseg): ...to here.
---
 gnu/packages/bioconductor.scm   | 30 ++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 30 ------------------------------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4657b0fa8b..313ed7e36f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2236,6 +2236,36 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
 CAGE.")
     (license license:gpl2+)))
 
+(define-public r-fastseg
+  (package
+    (name "r-fastseg")
+    (version "1.36.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "fastseg" version))
+       (sha256
+        (base32
+         "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
+    (synopsis "Fast segmentation algorithm for genetic sequencing data")
+    (description
+     "Fastseg implements a very fast and efficient segmentation algorithm.
+It can segment data from DNA microarrays and data from next generation
+sequencing for example to detect copy number segments.  Further it can segment
+data from RNA microarrays like tiling arrays to identify transcripts.  Most
+generally, it can segment data given as a matrix or as a vector.  Various data
+formats can be used as input to fastseg like expression set objects for
+microarrays or GRanges for sequencing data.")
+    (license license:lgpl2.0+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1dc2d6f977..33680c283d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9022,36 +9022,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-fastseg
-  (package
-    (name "r-fastseg")
-    (version "1.36.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "fastseg" version))
-       (sha256
-        (base32
-         "1ln6w93ag4wanp0nrm0pqngbfc88w95zq2kcj583hbxy885dkg4f"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://www.bioinf.jku.at/software/fastseg/index.html")
-    (synopsis "Fast segmentation algorithm for genetic sequencing data")
-    (description
-     "Fastseg implements a very fast and efficient segmentation algorithm.
-It can segment data from DNA microarrays and data from next generation
-sequencing for example to detect copy number segments.  Further it can segment
-data from RNA microarrays like tiling arrays to identify transcripts.  Most
-generally, it can segment data given as a matrix or as a vector.  Various data
-formats can be used as input to fastseg like expression set objects for
-microarrays or GRanges for sequencing data.")
-    (license license:lgpl2.0+)))
-
 (define-public r-keggrest
   (package
     (name "r-keggrest")
-- 
2.30.1

[bug#48575] [PATCH 22/50] gnu: r-affy: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-affy): Move from here...
* gnu/packages/bioconductor.scm (r-affy): ...to here.
---
 gnu/packages/bioconductor.scm   | 28 ++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 28 ----------------------------
 2 files changed, 28 insertions(+), 28 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 313ed7e36f..6d60b5884c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1550,6 +1550,34 @@ optimized in C++, and the main interface function provides an easy way of
 performing parallel computations on multicore machines.")
     (license license:gpl2+)))
 
+(define-public r-affy
+  (package
+    (name "r-affy")
+    (version "1.68.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affy" version))
+       (sha256
+        (base32
+         "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affyio" ,r-affyio)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-preprocesscore" ,r-preprocesscore)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://bioconductor.org/packages/affy")
+    (synopsis "Methods for affymetrix oligonucleotide arrays")
+    (description
+     "This package contains functions for exploratory oligonucleotide array
+analysis.")
+    (license license:lgpl2.0+)))
+
 (define-public r-affycomp
   (package
     (name "r-affycomp")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 33680c283d..b789ecd977 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8958,34 +8958,6 @@ upon file format information.  The primary focus is on accessing the CEL and
 CDF file formats.")
     (license license:lgpl2.0+)))
 
-(define-public r-affy
-  (package
-    (name "r-affy")
-    (version "1.68.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "affy" version))
-       (sha256
-        (base32
-         "0ywz548cbzk2k1njnxhlk5ydzvz2dk78ka8kx53gwrmdc4sc2b06"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affyio" ,r-affyio)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-preprocesscore" ,r-preprocesscore)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "https://bioconductor.org/packages/affy")
-    (synopsis "Methods for affymetrix oligonucleotide arrays")
-    (description
-     "This package contains functions for exploratory oligonucleotide array
-analysis.")
-    (license license:lgpl2.0+)))
-
 (define-public r-vsn
   (package
     (name "r-vsn")
-- 
2.30.1

[bug#48575] [PATCH 23/50] gnu: r-keggrest: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-keggrest): Move from here...
* gnu/packages/bioconductor.scm (r-keggrest): ...to here.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 26 --------------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6d60b5884c..5ee670e858 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2634,6 +2634,32 @@ microarray data, using nearest neighbor averaging.")
 Shiny-based display methods for Bioconductor objects.")
     (license license:artistic2.0)))
 
+(define-public r-keggrest
+  (package
+    (name "r-keggrest")
+    (version "1.30.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "KEGGREST" version))
+       (sha256
+        (base32
+         "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
+    (properties `((upstream-name . "KEGGREST")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-httr" ,r-httr)
+       ("r-png" ,r-png)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/KEGGREST")
+    (synopsis "Client-side REST access to KEGG")
+    (description
+     "This package provides a package that provides a client interface to the
+@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
+    (license license:artistic2.0)))
+
 (define-public r-limma
   (package
     (name "r-limma")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b789ecd977..5dacf8a342 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,32 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-keggrest
-  (package
-    (name "r-keggrest")
-    (version "1.30.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "KEGGREST" version))
-       (sha256
-        (base32
-         "0k9z85xf9la2y98xqmdmjb8mci9fh2fdybkl77x1yl26hyalip0s"))))
-    (properties `((upstream-name . "KEGGREST")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-httr" ,r-httr)
-       ("r-png" ,r-png)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/KEGGREST")
-    (synopsis "Client-side REST access to KEGG")
-    (description
-     "This package provides a package that provides a client interface to the
-@dfn{Kyoto Encyclopedia of Genes and Genomes} (KEGG) REST server.")
-    (license license:artistic2.0)))
-
 (define-public r-gage
   (package
     (name "r-gage")
-- 
2.30.1

[bug#48575] [PATCH 24/50] gnu: r-gage: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-gage): Move from here...
* gnu/packages/bioconductor.scm (r-gage): ...to here.
---
 gnu/packages/bioconductor.scm   | 33 ++++++++++++++++++++++++++++++++-
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ee670e858..f6d3ef897a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -4,7 +4,7 @@
 ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
-;;; Copyright © 2017, 2018, 2019, 2020 Tobias Geerinckx-Rice <me@tobias.gr>
+;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
 ;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
@@ -2294,6 +2294,37 @@ formats can be used as input to fastseg like expression set objects for
 microarrays or GRanges for sequencing data.")
     (license license:lgpl2.0+)))
 
+(define-public r-gage
+  (package
+    (name "r-gage")
+    (version "2.40.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "gage" version))
+       (sha256
+        (base32
+         "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-go-db" ,r-go-db)
+       ("r-graph" ,r-graph)
+       ("r-keggrest" ,r-keggrest)))
+    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
+                              "articles/10.1186/1471-2105-10-161"))
+    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
+    (description
+     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
+analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
+data attributes including sample sizes, experimental designs, assay platforms,
+and other types of heterogeneity.  The gage package provides functions for
+basic GAGE analysis, result processing and presentation.  In addition, it
+provides demo microarray data and commonly used gene set data based on KEGG
+pathways and GO terms.  These functions and data are also useful for gene set
+analysis using other methods.")
+    (license license:gpl2+)))
+
 (define-public r-genefilter
   (package
     (name "r-genefilter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5dacf8a342..daf1fb6958 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,37 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-gage
-  (package
-    (name "r-gage")
-    (version "2.40.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "gage" version))
-       (sha256
-        (base32
-         "1bs0hx8sqiyl08dqn2zx31kbv5aci4xvrs71pplx2yxal3jf5178"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-go-db" ,r-go-db)
-       ("r-graph" ,r-graph)
-       ("r-keggrest" ,r-keggrest)))
-    (home-page (string-append "https://bmcbioinformatics.biomedcentral.com/"
-                              "articles/10.1186/1471-2105-10-161"))
-    (synopsis "Generally applicable gene-set enrichment for pathway analysis")
-    (description
-     "GAGE is a published method for gene set (enrichment or GSEA) or pathway
-analysis.  GAGE is generally applicable independent of microarray or RNA-Seq
-data attributes including sample sizes, experimental designs, assay platforms,
-and other types of heterogeneity.  The gage package provides functions for
-basic GAGE analysis, result processing and presentation.  In addition, it
-provides demo microarray data and commonly used gene set data based on KEGG
-pathways and GO terms.  These functions and data are also useful for gene set
-analysis using other methods.")
-    (license license:gpl2+)))
-
 (define-public r-genomicfiles
   (package
     (name "r-genomicfiles")
-- 
2.30.1

[bug#48575] [PATCH 25/50] gnu: r-complexheatmap: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-complexheatmap): Move from here...
* gnu/packages/bioconductor.scm (r-complexheatmap): ...to here.
---
 gnu/packages/bioconductor.scm   | 39 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 39 ---------------------------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f6d3ef897a..92eb5a0906 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2082,6 +2082,45 @@ genome data packages and support for efficient SNP representation.")
 analysis.")
     (license license:artistic2.0)))
 
+(define-public r-complexheatmap
+  (package
+    (name "r-complexheatmap")
+    (version "2.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ComplexHeatmap" version))
+       (sha256
+        (base32
+         "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
+    (properties
+     `((upstream-name . "ComplexHeatmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-cairo" ,r-cairo)
+       ("r-circlize" ,r-circlize)
+       ("r-clue" ,r-clue)
+       ("r-colorspace" ,r-colorspace)
+       ("r-digest" ,r-digest)
+       ("r-getoptlong" ,r-getoptlong)
+       ("r-globaloptions" ,r-globaloptions)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-png" ,r-png)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://github.com/jokergoo/ComplexHeatmap")
+    (synopsis "Making Complex Heatmaps")
+    (description
+     "Complex heatmaps are efficient to visualize associations between
+different sources of data sets and reveal potential structures.  This package
+provides a highly flexible way to arrange multiple heatmaps and supports
+self-defined annotation graphics.")
+    (license license:gpl2+)))
+
 (define-public r-deseq
   (package
     (name "r-deseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index daf1fb6958..acaf41acc4 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9028,45 +9028,6 @@ distributed by file or by range.  User defined mapper and reducer functions
 provide added flexibility for data combination and manipulation.")
     (license license:artistic2.0)))
 
-(define-public r-complexheatmap
-  (package
-    (name "r-complexheatmap")
-    (version "2.6.2")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ComplexHeatmap" version))
-       (sha256
-        (base32
-         "1nx1xxpq8zrvi990v9fmvx3msl85pdz5dp1gp6m78q6i4s2alg5x"))))
-    (properties
-     `((upstream-name . "ComplexHeatmap")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-cairo" ,r-cairo)
-       ("r-circlize" ,r-circlize)
-       ("r-clue" ,r-clue)
-       ("r-colorspace" ,r-colorspace)
-       ("r-digest" ,r-digest)
-       ("r-getoptlong" ,r-getoptlong)
-       ("r-globaloptions" ,r-globaloptions)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-png" ,r-png)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page
-     "https://github.com/jokergoo/ComplexHeatmap")
-    (synopsis "Making Complex Heatmaps")
-    (description
-     "Complex heatmaps are efficient to visualize associations between
-different sources of data sets and reveal potential structures.  This package
-provides a highly flexible way to arrange multiple heatmaps and supports
-self-defined annotation graphics.")
-    (license license:gpl2+)))
-
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-- 
2.30.1

[bug#48575] [PATCH 26/50] gnu: r-genomicfiles: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-genomicfiles): Move from here...
* gnu/packages/bioconductor.scm (r-genomicfiles): ...to here.
---
 gnu/packages/bioconductor.scm   | 34 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 34 ---------------------------------
 2 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 92eb5a0906..e73e78f616 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2546,6 +2546,40 @@ transcripts, exons, cds and genes.  Flexible methods are provided for
 extracting the desired features in a convenient format.")
     (license license:artistic2.0)))
 
+(define-public r-genomicfiles
+  (package
+    (name "r-genomicfiles")
+    (version "1.26.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GenomicFiles" version))
+       (sha256
+        (base32
+         "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
+    (properties `((upstream-name . "GenomicFiles")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixgenerics" ,r-matrixgenerics)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/GenomicFiles")
+    (synopsis "Distributed computing by file or by range")
+    (description
+     "This package provides infrastructure for parallel computations
+distributed by file or by range.  User defined mapper and reducer functions
+provide added flexibility for data combination and manipulation.")
+    (license license:artistic2.0)))
+
 (define-public r-genomicranges
   (package
     (name "r-genomicranges")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index acaf41acc4..4836eee82c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,40 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-genomicfiles
-  (package
-    (name "r-genomicfiles")
-    (version "1.26.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "GenomicFiles" version))
-       (sha256
-        (base32
-         "0awnf0m1pz7cw9wvh9cfxz9k7xm6wnvjm7xbxf139lrhd4nlyqjz"))))
-    (properties `((upstream-name . "GenomicFiles")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixgenerics" ,r-matrixgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/GenomicFiles")
-    (synopsis "Distributed computing by file or by range")
-    (description
-     "This package provides infrastructure for parallel computations
-distributed by file or by range.  User defined mapper and reducer functions
-provide added flexibility for data combination and manipulation.")
-    (license license:artistic2.0)))
-
 (define-public r-dirichletmultinomial
   (package
     (name "r-dirichletmultinomial")
-- 
2.30.1

[bug#48575] [PATCH 27/50] gnu: r-dirichletmultinomial: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-dirichletmultinomial): Move from here...
* gnu/packages/bioconductor.scm (r-dirichletmultinomial): ...to here.
---
 gnu/packages/bioconductor.scm   | 29 +++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 29 -----------------------------
 2 files changed, 29 insertions(+), 29 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e73e78f616..7717c821b9 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2235,6 +2235,35 @@ testing.  The package also provides functions for the visualization and
 exploration of the results.")
     (license license:gpl3+)))
 
+(define-public r-dirichletmultinomial
+  (package
+    (name "r-dirichletmultinomial")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "DirichletMultinomial" version))
+       (sha256
+        (base32
+         "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
+    (properties
+     `((upstream-name . "DirichletMultinomial")))
+    (build-system r-build-system)
+    (inputs
+     `(("gsl" ,gsl)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-iranges" ,r-iranges)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/DirichletMultinomial")
+    (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
+    (description
+     "Dirichlet-multinomial mixture models can be used to describe variability
+in microbial metagenomic data.  This package is an interface to code
+originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
+1-15.")
+    (license license:lgpl3)))
+
 (define-public r-edaseq
   (package
     (name "r-edaseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4836eee82c..0c7b3d602f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8994,35 +8994,6 @@ their variance is independent of the mean, and they are usually more sensitive
 and specific in detecting differential transcription.")
     (license license:artistic2.0)))
 
-(define-public r-dirichletmultinomial
-  (package
-    (name "r-dirichletmultinomial")
-    (version "1.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "DirichletMultinomial" version))
-       (sha256
-        (base32
-         "098zql6ryd1b0gkq4cjybblyh0x8xidxxfygqq5a5x9asl8y4vsk"))))
-    (properties
-     `((upstream-name . "DirichletMultinomial")))
-    (build-system r-build-system)
-    (inputs
-     `(("gsl" ,gsl)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-iranges" ,r-iranges)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/DirichletMultinomial")
-    (synopsis "Dirichlet-Multinomial mixture models for microbiome data")
-    (description
-     "Dirichlet-multinomial mixture models can be used to describe variability
-in microbial metagenomic data.  This package is an interface to code
-originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2):
-1-15.")
-    (license license:lgpl3)))
-
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-- 
2.30.1

[bug#48575] [PATCH 28/50] gnu: r-organismdbi: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-organismdbi): Move from here...
* gnu/packages/bioconductor.scm (r-organismdbi): ...to here.
---
 gnu/packages/bioconductor.scm   | 32 ++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 32 --------------------------------
 2 files changed, 32 insertions(+), 32 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7717c821b9..c63d39dc9c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2940,6 +2940,38 @@ mzIdentML files with the drawback of having less pretty output than a vendor
 specific parser.")
     (license license:gpl2+)))
 
+(define-public r-organismdbi
+  (package
+    (name "r-organismdbi")
+    (version "1.32.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "OrganismDbi" version))
+       (sha256
+        (base32
+         "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
+    (properties `((upstream-name . "OrganismDbi")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biocmanager" ,r-biocmanager)
+       ("r-dbi" ,r-dbi)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-graph" ,r-graph)
+       ("r-iranges" ,r-iranges)
+       ("r-rbgl" ,r-rbgl)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://bioconductor.org/packages/OrganismDbi")
+    (synopsis "Software to enable the smooth interfacing of database packages")
+    (description "The package enables a simple unified interface to several
+annotation packages each of which has its own schema by taking advantage of
+the fact that each of these packages implements a select methods.")
+    (license license:artistic2.0)))
+
 (define-public r-pcamethods
   (package
     (name "r-pcamethods")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0c7b3d602f..1c90700c95 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -9039,38 +9039,6 @@ chromosome region or transcript models of lincRNA genes.")
     ;; No version specified
     (license license:lgpl3+)))
 
-(define-public r-organismdbi
-  (package
-    (name "r-organismdbi")
-    (version "1.32.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "OrganismDbi" version))
-       (sha256
-        (base32
-         "1mklnzs0d0ygcdibwfnk5xqr8ln6wpa00qcaw9c68m342kql0jqw"))))
-    (properties `((upstream-name . "OrganismDbi")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biocmanager" ,r-biocmanager)
-       ("r-dbi" ,r-dbi)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-graph" ,r-graph)
-       ("r-iranges" ,r-iranges)
-       ("r-rbgl" ,r-rbgl)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://bioconductor.org/packages/OrganismDbi")
-    (synopsis "Software to enable the smooth interfacing of database packages")
-    (description "The package enables a simple unified interface to several
-annotation packages each of which has its own schema by taking advantage of
-the fact that each of these packages implements a select methods.")
-    (license license:artistic2.0)))
-
 (define-public r-biovizbase
   (package
     (name "r-biovizbase")
-- 
2.30.1

[bug#48575] [PATCH 29/50] gnu: r-affyio: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-affyio): Move from here...
* gnu/packages/bioconductor.scm (r-affyio): ...to here.
---
 gnu/packages/bioconductor.scm   | 24 ++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 24 ------------------------
 2 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c63d39dc9c..d0ebcf8481 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1694,6 +1694,30 @@ problems in CEL-level data to help evaluate performance of quality metrics.")
 to streamline the more common analyses that a Biostatistician might see.")
     (license license:artistic2.0)))
 
+(define-public r-affyio
+  (package
+    (name "r-affyio")
+    (version "1.60.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "affyio" version))
+       (sha256
+        (base32
+         "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-zlibbioc" ,r-zlibbioc)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (home-page "https://github.com/bmbolstad/affyio")
+    (synopsis "Tools for parsing Affymetrix data files")
+    (description
+     "This package provides routines for parsing Affymetrix data files based
+upon file format information.  The primary focus is on accessing the CEL and
+CDF file formats.")
+    (license license:lgpl2.0+)))
+
 (define-public r-affxparser
   (package
     (name "r-affxparser")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1c90700c95..7256df3f83 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,30 +8934,6 @@ proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
-(define-public r-affyio
-  (package
-    (name "r-affyio")
-    (version "1.60.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "affyio" version))
-       (sha256
-        (base32
-         "14xnzrxrvgxgixjhq5a9fdgcmrxam2j74hwidkc9if92ffv6s83h"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-zlibbioc" ,r-zlibbioc)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (home-page "https://github.com/bmbolstad/affyio")
-    (synopsis "Tools for parsing Affymetrix data files")
-    (description
-     "This package provides routines for parsing Affymetrix data files based
-upon file format information.  The primary focus is on accessing the CEL and
-CDF file formats.")
-    (license license:lgpl2.0+)))
-
 (define-public r-vsn
   (package
     (name "r-vsn")
-- 
2.30.1

[bug#48575] [PATCH 30/50] gnu: r-vsn: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-vsn): Move from here...
* gnu/packages/bioconductor.scm (r-vsn): ...to here.
---
 gnu/packages/bioconductor.scm   | 36 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 36 ---------------------------------
 2 files changed, 36 insertions(+), 36 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d0ebcf8481..05c4896276 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3480,6 +3480,42 @@ dependencies between GO terms can be implemented and applied.")
 coding changes and predict coding outcomes.")
     (license license:artistic2.0)))
 
+(define-public r-vsn
+  (package
+    (name "r-vsn")
+    (version "3.58.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "vsn" version))
+       (sha256
+        (base32
+         "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-affy" ,r-affy)
+       ("r-biobase" ,r-biobase)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-lattice" ,r-lattice)
+       ("r-limma" ,r-limma)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
+    (synopsis "Variance stabilization and calibration for microarray data")
+    (description
+     "The package implements a method for normalising microarray intensities,
+and works for single- and multiple-color arrays.  It can also be used for data
+from other technologies, as long as they have similar format.  The method uses
+a robust variant of the maximum-likelihood estimator for an
+additive-multiplicative error model and affine calibration.  The model
+incorporates data calibration step (a.k.a.  normalization), a model for the
+dependence of the variance on the mean intensity and a variance stabilizing
+data transformation.  Differences between transformed intensities are
+analogous to \"normalized log-ratios\".  However, in contrast to the latter,
+their variance is independent of the mean, and they are usually more sensitive
+and specific in detecting differential transcription.")
+    (license license:artistic2.0)))
+
 (define-public r-xvector
   (package
     (name "r-xvector")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7256df3f83..600c2ca81e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,42 +8934,6 @@ proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
-(define-public r-vsn
-  (package
-    (name "r-vsn")
-    (version "3.58.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "vsn" version))
-       (sha256
-        (base32
-         "0dfrfflidpnphwyqzmmfiz9blfqv6qa09xlwgfabhpfsf3ml2rlb"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-affy" ,r-affy)
-       ("r-biobase" ,r-biobase)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-lattice" ,r-lattice)
-       ("r-limma" ,r-limma)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
-    (home-page "https://bioconductor.org/packages/release/bioc/html/vsn.html")
-    (synopsis "Variance stabilization and calibration for microarray data")
-    (description
-     "The package implements a method for normalising microarray intensities,
-and works for single- and multiple-color arrays.  It can also be used for data
-from other technologies, as long as they have similar format.  The method uses
-a robust variant of the maximum-likelihood estimator for an
-additive-multiplicative error model and affine calibration.  The model
-incorporates data calibration step (a.k.a.  normalization), a model for the
-dependence of the variance on the mean intensity and a variance stabilizing
-data transformation.  Differences between transformed intensities are
-analogous to \"normalized log-ratios\".  However, in contrast to the latter,
-their variance is independent of the mean, and they are usually more sensitive
-and specific in detecting differential transcription.")
-    (license license:artistic2.0)))
-
 (define-public r-ensembldb
   (package
     (name "r-ensembldb")
-- 
2.30.1

[bug#48575] [PATCH 31/50] gnu: r-biovizbase: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-biovizbase): Move from here...
* gnu/packages/bioconductor.scm (r-biovizbase): ...to here.
---
 gnu/packages/bioconductor.scm   | 42 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 42 ---------------------------------
 2 files changed, 42 insertions(+), 42 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 05c4896276..7439ad96da 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2044,6 +2044,48 @@ matching algorithms, and other utilities, for fast manipulation of large
 biological sequences or sets of sequences.")
     (license license:artistic2.0)))
 
+(define-public r-biovizbase
+  (package
+    (name "r-biovizbase")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "biovizBase" version))
+       (sha256
+        (base32
+         "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
+    (properties `((upstream-name . "biovizBase")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-dichromat" ,r-dichromat)
+       ("r-ensembldb" ,r-ensembldb)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-hmisc" ,r-hmisc)
+       ("r-iranges" ,r-iranges)
+       ("r-rcolorbrewer" ,r-rcolorbrewer)
+       ("r-rlang" ,r-rlang)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-scales" ,r-scales)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/biovizBase")
+    (synopsis "Basic graphic utilities for visualization of genomic data")
+    (description
+     "The biovizBase package is designed to provide a set of utilities, color
+schemes and conventions for genomic data.  It serves as the base for various
+high-level packages for biological data visualization.  This saves development
+effort and encourages consistency.")
+    (license license:artistic2.0)))
+
 (define-public r-bsgenome
   (package
     (name "r-bsgenome")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 600c2ca81e..e6692ece0c 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8979,48 +8979,6 @@ chromosome region or transcript models of lincRNA genes.")
     ;; No version specified
     (license license:lgpl3+)))
 
-(define-public r-biovizbase
-  (package
-    (name "r-biovizbase")
-    (version "1.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "biovizBase" version))
-       (sha256
-        (base32
-         "10jflvadfcgxq2jnfxkpn417xd8ibh3zllz9rsqnq5w3wgfr4fhq"))))
-    (properties `((upstream-name . "biovizBase")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-dichromat" ,r-dichromat)
-       ("r-ensembldb" ,r-ensembldb)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-hmisc" ,r-hmisc)
-       ("r-iranges" ,r-iranges)
-       ("r-rcolorbrewer" ,r-rcolorbrewer)
-       ("r-rlang" ,r-rlang)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-scales" ,r-scales)
-       ("r-summarizedexperiment" ,r-summarizedexperiment)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/biovizBase")
-    (synopsis "Basic graphic utilities for visualization of genomic data")
-    (description
-     "The biovizBase package is designed to provide a set of utilities, color
-schemes and conventions for genomic data.  It serves as the base for various
-high-level packages for biological data visualization.  This saves development
-effort and encourages consistency.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.30.1

[bug#48575] [PATCH 32/50] gnu: r-ensembldb: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-ensembldb): Move from here...
* gnu/packages/bioconductor.scm (r-ensembldb): ...to here.
---
 gnu/packages/bioconductor.scm   | 45 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 45 ---------------------------------
 2 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7439ad96da..7e86af7d21 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2398,6 +2398,51 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and
 CAGE.")
     (license license:gpl2+)))
 
+(define-public r-ensembldb
+  (package
+    (name "r-ensembldb")
+    (version "2.14.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ensembldb" version))
+       (sha256
+        (base32
+         "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-annotationdbi" ,r-annotationdbi)
+       ("r-annotationfilter" ,r-annotationfilter)
+       ("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-curl" ,r-curl)
+       ("r-dbi" ,r-dbi)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/jotsetung/ensembldb")
+    (synopsis "Utilities to create and use Ensembl-based annotation databases")
+    (description
+     "The package provides functions to create and use transcript-centric
+annotation databases/packages.  The annotation for the databases are directly
+fetched from Ensembl using their Perl API.  The functionality and data is
+similar to that of the TxDb packages from the @code{GenomicFeatures} package,
+but, in addition to retrieve all gene/transcript models and annotations from
+the database, the @code{ensembldb} package also provides a filter framework
+allowing to retrieve annotations for specific entries like genes encoded on a
+chromosome region or transcript models of lincRNA genes.")
+    ;; No version specified
+    (license license:lgpl3+)))
+
 (define-public r-fastseg
   (package
     (name "r-fastseg")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e6692ece0c..baef88cd2e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8934,51 +8934,6 @@ proteowizard library for mzML and mzIdentML.  The netCDF reading code has
 previously been used in XCMS.")
     (license license:artistic2.0)))
 
-(define-public r-ensembldb
-  (package
-    (name "r-ensembldb")
-    (version "2.14.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ensembldb" version))
-       (sha256
-        (base32
-         "1hxwfh19qafpdhzprvw4nr8ks3gz7f0y8gyfhk8yqmmvvnvgqv40"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-annotationdbi" ,r-annotationdbi)
-       ("r-annotationfilter" ,r-annotationfilter)
-       ("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-curl" ,r-curl)
-       ("r-dbi" ,r-dbi)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/jotsetung/ensembldb")
-    (synopsis "Utilities to create and use Ensembl-based annotation databases")
-    (description
-     "The package provides functions to create and use transcript-centric
-annotation databases/packages.  The annotation for the databases are directly
-fetched from Ensembl using their Perl API.  The functionality and data is
-similar to that of the TxDb packages from the @code{GenomicFeatures} package,
-but, in addition to retrieve all gene/transcript models and annotations from
-the database, the @code{ensembldb} package also provides a filter framework
-allowing to retrieve annotations for specific entries like genes encoded on a
-chromosome region or transcript models of lincRNA genes.")
-    ;; No version specified
-    (license license:lgpl3+)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.30.1

[bug#48575] [PATCH 33/50] gnu: r-mzr: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-mzr): Move from here...
* gnu/packages/bioconductor.scm (r-mzr): ...to here.
---
 gnu/packages/bioconductor.scm   | 62 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 61 --------------------------------
 2 files changed, 62 insertions(+), 61 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7e86af7d21..5ceffd7b4d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -36,6 +36,7 @@
   #:use-module (gnu packages)
   #:use-module (gnu packages base)
   #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages boost)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages gcc)
@@ -3051,6 +3052,67 @@ mzIdentML files with the drawback of having less pretty output than a vendor
 specific parser.")
     (license license:gpl2+)))
 
+(define-public r-mzr
+  (package
+    (name "r-mzr")
+    (version "2.24.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "mzR" version))
+       (sha256
+        (base32
+         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
+       (modules '((guix build utils)))
+       (snippet
+        '(begin
+           (delete-file-recursively "src/boost")
+           #t))))
+    (properties `((upstream-name . "mzR")))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'use-system-boost
+           (lambda _
+             (substitute* "src/Makevars"
+               (("\\./boost/libs.*") "")
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a"))
+               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
+               (("\\ARCH_OBJS=" line)
+                (string-append line
+                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
+-lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
+             #t)))))
+    (inputs
+     `(;; Our default boost package won't work here, unfortunately, even with
+       ;; mzR version 2.24.1.
+       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
+       ("zlib" ,zlib)))
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biocgenerics" ,r-biocgenerics)
+       ("r-ncdf4" ,r-ncdf4)
+       ("r-protgenerics" ,r-protgenerics)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhdf5lib" ,r-rhdf5lib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/sneumann/mzR/")
+    (synopsis "Parser for mass spectrometry data files")
+    (description
+     "The mzR package provides a unified API to the common file formats and
+parsers available for mass spectrometry data.  It comes with a wrapper for the
+ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
+The package contains the original code written by the ISB, and a subset of the
+proteowizard library for mzML and mzIdentML.  The netCDF reading code has
+previously been used in XCMS.")
+    (license license:artistic2.0)))
+
 (define-public r-organismdbi
   (package
     (name "r-organismdbi")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index baef88cd2e..a6321a179a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8873,67 +8873,6 @@ trait.")
 proteomics packages.")
     (license license:artistic2.0)))
 
-(define-public r-mzr
-  (package
-    (name "r-mzr")
-    (version "2.24.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "mzR" version))
-       (sha256
-        (base32
-         "0ik0yrjhvk8r5pm990chn2aadp0gqzzkkm0027682ky34xp142sg"))
-       (modules '((guix build utils)))
-       (snippet
-        '(begin
-           (delete-file-recursively "src/boost")
-           #t))))
-    (properties `((upstream-name . "mzR")))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'use-system-boost
-           (lambda _
-             (substitute* "src/Makevars"
-               (("\\./boost/libs.*") "")
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a"))
-               (("PKG_LIBS=") "PKG_LIBS=$(BOOST_LIBS) ")
-               (("\\ARCH_OBJS=" line)
-                (string-append line
-                               "\nBOOST_LIBS=-lboost_system -lboost_regex \
--lboost_iostreams -lboost_thread -lboost_filesystem -lboost_chrono\n")))
-             #t)))))
-    (inputs
-     `(;; Our default boost package won't work here, unfortunately, even with
-       ;; mzR version 2.24.1.
-       ("boost" ,boost-for-mysql) ; use this instead of the bundled boost sources
-       ("zlib" ,zlib)))
-    (propagated-inputs
-     `(("r-biobase" ,r-biobase)
-       ("r-biocgenerics" ,r-biocgenerics)
-       ("r-ncdf4" ,r-ncdf4)
-       ("r-protgenerics" ,r-protgenerics)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhdf5lib" ,r-rhdf5lib)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/sneumann/mzR/")
-    (synopsis "Parser for mass spectrometry data files")
-    (description
-     "The mzR package provides a unified API to the common file formats and
-parsers available for mass spectrometry data.  It comes with a wrapper for the
-ISB random access parser for mass spectrometry mzXML, mzData and mzML files.
-The package contains the original code written by the ISB, and a subset of the
-proteowizard library for mzML and mzIdentML.  The netCDF reading code has
-previously been used in XCMS.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.30.1

[bug#48575] [PATCH 34/50] gnu: r-protgenerics: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-protgenerics): Move from here...
* gnu/packages/bioconductor.scm (r-protgenerics): ...to here.
---
 gnu/packages/bioconductor.scm   | 20 ++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 20 --------------------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 5ceffd7b4d..a9365a4018 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3175,6 +3175,26 @@ the results is also provided.  All PCA methods make use of the same data
 structure (pcaRes) to provide a common interface to the PCA results.")
     (license license:gpl3+)))
 
+(define-public r-protgenerics
+  (package
+    (name "r-protgenerics")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "ProtGenerics" version))
+       (sha256
+        (base32
+         "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
+    (properties `((upstream-name . "ProtGenerics")))
+    (build-system r-build-system)
+    (home-page "https://github.com/lgatto/ProtGenerics")
+    (synopsis "S4 generic functions for proteomics infrastructure")
+    (description
+     "This package provides S4 generic functions needed by Bioconductor
+proteomics packages.")
+    (license license:artistic2.0)))
+
 (define-public r-rbgl
   (package
     (name "r-rbgl")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a6321a179a..6120cb6804 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8853,26 +8853,6 @@ for analyzing gene-level association tests in meta-analyses for binary
 trait.")
     (license license:gpl3)))
 
-(define-public r-protgenerics
-  (package
-    (name "r-protgenerics")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "ProtGenerics" version))
-       (sha256
-        (base32
-         "0yihxphgkshvfv1sn67wc4zvr2zlzws2j7ki3zabm6vyfkfdkfiz"))))
-    (properties `((upstream-name . "ProtGenerics")))
-    (build-system r-build-system)
-    (home-page "https://github.com/lgatto/ProtGenerics")
-    (synopsis "S4 generic functions for proteomics infrastructure")
-    (description
-     "This package provides S4 generic functions needed by Bioconductor
-proteomics packages.")
-    (license license:artistic2.0)))
-
 (define-public r-dropbead
   (let ((commit "d746c6f3b32110428ea56d6a0001ce52a251c247")
         (revision "2"))
-- 
2.30.1

[bug#48575] [PATCH 35/50] gnu: r-sva: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-sva): Move from here...
* gnu/packages/bioconductor.scm (r-sva): ...to here.
---
 gnu/packages/bioconductor.scm   | 31 +++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 31 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a9365a4018..a7b1c63b56 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3524,6 +3524,37 @@ typically represent genomic ranges of interest and the columns represent
 samples.")
     (license license:artistic2.0)))
 
+(define-public r-sva
+  (package
+    (name "r-sva")
+    (version "3.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "sva" version))
+       (sha256
+        (base32
+         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-edger" ,r-edger)
+       ("r-genefilter" ,r-genefilter)
+       ("r-mgcv" ,r-mgcv)
+       ("r-biocparallel" ,r-biocparallel)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-limma" ,r-limma)))
+    (home-page "https://bioconductor.org/packages/sva")
+    (synopsis "Surrogate variable analysis")
+    (description
+     "This package contains functions for removing batch effects and other
+unwanted variation in high-throughput experiment.  It also contains functions
+for identifying and building surrogate variables for high-dimensional data
+sets.  Surrogate variables are covariates constructed directly from
+high-dimensional data like gene expression/RNA sequencing/methylation/brain
+imaging data that can be used in subsequent analyses to adjust for unknown,
+unmodeled, or latent sources of noise.")
+    (license license:artistic2.0)))
+
 (define-public r-systempiper
   (package
     (name "r-systempiper")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6120cb6804..2cc41b7e98 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8790,37 +8790,6 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and
 TAB-Seq.")
     (license license:artistic2.0)))
 
-(define-public r-sva
-  (package
-    (name "r-sva")
-    (version "3.38.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "sva" version))
-       (sha256
-        (base32
-         "1hpzzg3qrgkd8kwg1m5gq94cikjgk9j4l1wk58fxl49s6fmd13zy"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-edger" ,r-edger)
-       ("r-genefilter" ,r-genefilter)
-       ("r-mgcv" ,r-mgcv)
-       ("r-biocparallel" ,r-biocparallel)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-limma" ,r-limma)))
-    (home-page "https://bioconductor.org/packages/sva")
-    (synopsis "Surrogate variable analysis")
-    (description
-     "This package contains functions for removing batch effects and other
-unwanted variation in high-throughput experiment.  It also contains functions
-for identifying and building surrogate variables for high-dimensional data
-sets.  Surrogate variables are covariates constructed directly from
-high-dimensional data like gene expression/RNA sequencing/methylation/brain
-imaging data that can be used in subsequent analyses to adjust for unknown,
-unmodeled, or latent sources of noise.")
-    (license license:artistic2.0)))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
-- 
2.30.1

[bug#48575] [PATCH 36/50] gnu: r-motifrg: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-motifrg): Move from here...
* gnu/packages/bioconductor.scm (r-motifrg): ...to here.
---
 gnu/packages/bioconductor.scm   | 27 +++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 27 ---------------------------
 2 files changed, 27 insertions(+), 27 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index a7b1c63b56..47a245b4f5 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2924,6 +2924,33 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-motifrg
+  (package
+    (name "r-motifrg")
+    (version "1.31.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "motifRG" version))
+       (sha256
+        (base32
+         "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
+    (properties `((upstream-name . "motifRG")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-iranges" ,r-iranges)
+       ("r-seqlogo" ,r-seqlogo)
+       ("r-xvector" ,r-xvector)))
+    (home-page "https://bioconductor.org/packages/motifRG")
+    (synopsis "Discover motifs in high throughput sequencing data")
+    (description
+     "This package provides tools for discriminative motif discovery in high
+throughput genetic sequencing data sets using regression methods.")
+    (license license:artistic2.0)))
+
 (define-public r-msnbase
   (package
     (name "r-msnbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2cc41b7e98..e2000ccb68 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,33 +7872,6 @@ plots the corresponding sequence logo as introduced by Schneider and
 Stephens (1990).")
     (license license:lgpl2.0+)))
 
-(define-public r-motifrg
-  (package
-    (name "r-motifrg")
-    (version "1.31.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "motifRG" version))
-       (sha256
-        (base32
-         "1ml6zyzlk8yjbnfhga2qnw8nl43rankvka0kc1yljxr2b66aqbhn"))))
-    (properties `((upstream-name . "motifRG")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-iranges" ,r-iranges)
-       ("r-seqlogo" ,r-seqlogo)
-       ("r-xvector" ,r-xvector)))
-    (home-page "https://bioconductor.org/packages/motifRG")
-    (synopsis "Discover motifs in high throughput sequencing data")
-    (description
-     "This package provides tools for discriminative motif discovery in high
-throughput genetic sequencing data sets using regression methods.")
-    (license license:artistic2.0)))
-
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-- 
2.30.1

[bug#48575] [PATCH 37/50] gnu: r-seqlogo: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-seqlogo): Move from here...
* gnu/packages/bioconductor.scm (r-seqlogo): ...to here.
---
 gnu/packages/bioconductor.scm   | 23 +++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 23 -----------------------
 2 files changed, 23 insertions(+), 23 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 47a245b4f5..c58c5af5d6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3447,6 +3447,29 @@ differential expression analysis, RNAseq data and related problems.")
     ;; Any version of the LGPL
     (license license:lgpl3+)))
 
+(define-public r-seqlogo
+  (package
+    (name "r-seqlogo")
+    (version "1.56.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "seqLogo" version))
+       (sha256
+        (base32
+         "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
+    (properties `((upstream-name . "seqLogo")))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/seqLogo")
+    (synopsis "Sequence logos for DNA sequence alignments")
+    (description
+     "seqLogo takes the position weight matrix of a DNA sequence motif and
+plots the corresponding sequence logo as introduced by Schneider and
+Stephens (1990).")
+    (license license:lgpl2.0+)))
+
 (define-public r-seqpattern
   (package
     (name "r-seqpattern")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e2000ccb68..9ba818d581 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,29 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-seqlogo
-  (package
-    (name "r-seqlogo")
-    (version "1.56.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "seqLogo" version))
-       (sha256
-        (base32
-         "02rpzjjfg5chlwwfbvv72cm78cg2vfmdwzars0cin9hz1hd7rnq1"))))
-    (properties `((upstream-name . "seqLogo")))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/seqLogo")
-    (synopsis "Sequence logos for DNA sequence alignments")
-    (description
-     "seqLogo takes the position weight matrix of a DNA sequence motif and
-plots the corresponding sequence logo as introduced by Schneider and
-Stephens (1990).")
-    (license license:lgpl2.0+)))
-
 (define-public r-zlibbioc
   (package
     (name "r-zlibbioc")
-- 
2.30.1

[bug#48575] [PATCH 38/50] gnu: r-zlibbioc: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-zlibbioc): Move from here...
* gnu/packages/bioconductor.scm (r-zlibbioc): ...to here.
---
 gnu/packages/bioconductor.scm   | 19 +++++++++++++++++++
 gnu/packages/bioinformatics.scm | 19 -------------------
 2 files changed, 19 insertions(+), 19 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index c58c5af5d6..e720d7bf6a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3802,6 +3802,25 @@ and specific in detecting differential transcription.")
 \"externally\" (behind an R external pointer, or on disk).")
     (license license:artistic2.0)))
 
+  (define-public r-zlibbioc
+  (package
+    (name "r-zlibbioc")
+    (version "1.36.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "zlibbioc" version))
+              (sha256
+               (base32
+                "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
+    (properties
+     `((upstream-name . "zlibbioc")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/zlibbioc")
+    (synopsis "Provider for zlib-1.2.5 to R packages")
+    (description "This package uses the source code of zlib-1.2.5 to create
+libraries for systems that do not have these available via other means.")
+    (license license:artistic2.0)))
+
 (define-public r-geneplotter
   (package
     (name "r-geneplotter")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 9ba818d581..39c437f4a2 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7849,25 +7849,6 @@ including VCF header and contents in RDF and JSON.")
     (home-page "https://github.com/vcflib/bio-vcf")
     (license license:expat)))
 
-(define-public r-zlibbioc
-  (package
-    (name "r-zlibbioc")
-    (version "1.36.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "zlibbioc" version))
-              (sha256
-               (base32
-                "0m36ddss0znvm19dhnxcclxjhgjplw8ajk8v419h20ab8an6khxg"))))
-    (properties
-     `((upstream-name . "zlibbioc")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/zlibbioc")
-    (synopsis "Provider for zlib-1.2.5 to R packages")
-    (description "This package uses the source code of zlib-1.2.5 to create
-libraries for systems that do not have these available via other means.")
-    (license license:artistic2.0)))
-
 (define-public r-r4rna
   (package
     (name "r-r4rna")
-- 
2.30.1

[bug#48575] [PATCH 39/50] gnu: r-rhtslib: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rhtslib): Move from here...
* gnu/packages/bioconductor.scm (r-rhtslib): ...to here.
---
 gnu/packages/bioconductor.scm   | 32 ++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 31 -------------------------------
 2 files changed, 32 insertions(+), 31 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e720d7bf6a..8e78a2a0ca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -39,6 +39,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages cran)
   #:use-module (gnu packages compression)
+  #:use-module (gnu packages curl)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages graphviz)
@@ -2832,6 +2833,37 @@ Enrichment Analysis} (GSEA).")
 the Human Protein Atlas project.")
     (license license:artistic2.0)))
 
+(define-public r-rhtslib
+  (package
+    (name "r-rhtslib")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Rhtslib" version))
+       (sha256
+        (base32
+         "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
+    (properties `((upstream-name . "Rhtslib")))
+    (build-system r-build-system)
+    ;; Without this a temporary directory ends up in the Rhtslib.so binary,
+    ;; which makes R abort the build.
+    (arguments '(#:configure-flags '("--no-staged-install")))
+    (propagated-inputs
+     `(("curl" ,curl)
+       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)
+       ("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/nhayden/Rhtslib")
+    (synopsis "High-throughput sequencing library as an R package")
+    (description
+     "This package provides the HTSlib C library for high-throughput
+nucleotide sequence analysis.  The package is primarily useful to developers
+of other R packages who wish to make use of HTSlib.")
+    (license license:lgpl2.0+)))
+
 (define-public r-impute
   (package
     (name "r-impute")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 39c437f4a2..586efcf21e 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,37 +7872,6 @@ including VCF header and contents in RDF and JSON.")
 secondary structure and comparative analysis in R.")
     (license license:gpl3+)))
 
-(define-public r-rhtslib
-  (package
-    (name "r-rhtslib")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "Rhtslib" version))
-       (sha256
-        (base32
-         "18wag2jnpda6078xjkpfdvar1gkb2myhw83gg03l39sabh35qya4"))))
-    (properties `((upstream-name . "Rhtslib")))
-    (build-system r-build-system)
-    ;; Without this a temporary directory ends up in the Rhtslib.so binary,
-    ;; which makes R abort the build.
-    (arguments '(#:configure-flags '("--no-staged-install")))
-    (propagated-inputs
-     `(("curl" ,curl)
-       ("zlib" ,zlib) ; packages using rhtslib need to link with zlib
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("pkg-config" ,pkg-config)
-       ("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/nhayden/Rhtslib")
-    (synopsis "High-throughput sequencing library as an R package")
-    (description
-     "This package provides the HTSlib C library for high-throughput
-nucleotide sequence analysis.  The package is primarily useful to developers
-of other R packages who wish to make use of HTSlib.")
-    (license license:lgpl2.0+)))
-
 (define-public r-bamsignals
   (package
     (name "r-bamsignals")
-- 
2.30.1

[bug#48575] [PATCH 40/50] gnu: r-bamsignals: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-bamsignals): Move from here...
* gnu/packages/bioconductor.scm (r-bamsignals): ...to here.
---
 gnu/packages/bioconductor.scm   | 30 ++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 30 ------------------------------
 2 files changed, 30 insertions(+), 30 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8e78a2a0ca..99607ba564 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1904,6 +1904,36 @@ standalone, be utilized in other packages, or be wrapped up in higher-level
 classes.")
     (license license:gpl2+)))
 
+(define-public r-bamsignals
+  (package
+    (name "r-bamsignals")
+    (version "1.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "bamsignals" version))
+       (sha256
+        (base32
+         "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/bamsignals")
+    (synopsis "Extract read count signals from bam files")
+    (description
+     "This package efficiently obtains count vectors from indexed bam
+files.  It counts the number of nucleotide sequence reads in given genomic
+ranges and it computes reads profiles and coverage profiles.  It also handles
+paired-end data.")
+    (license license:gpl2+)))
+
 (define-public r-biobase
   (package
     (name "r-biobase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 586efcf21e..ae61ecae74 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,36 +7872,6 @@ including VCF header and contents in RDF and JSON.")
 secondary structure and comparative analysis in R.")
     (license license:gpl3+)))
 
-(define-public r-bamsignals
-  (package
-    (name "r-bamsignals")
-    (version "1.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "bamsignals" version))
-       (sha256
-        (base32
-         "0p3r9z9z5sfkd0b951cgr751k4z0yviyn1jfw9d4fcnyld7g1jxv"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/bamsignals")
-    (synopsis "Extract read count signals from bam files")
-    (description
-     "This package efficiently obtains count vectors from indexed bam
-files.  It counts the number of nucleotide sequence reads in given genomic
-ranges and it computes reads profiles and coverage profiles.  It also handles
-paired-end data.")
-    (license license:gpl2+)))
-
 (define-public r-rcas
   (package
     (name "r-rcas")
-- 
2.30.1

[bug#48575] [PATCH 41/50] gnu: r-rcas: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rcas): Move from here...
* gnu/packages/bioconductor.scm (r-rcas): ...to here.
---
 gnu/packages/bioconductor.scm   | 49 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 49 ---------------------------------
 2 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 99607ba564..1d38fa1c05 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3307,6 +3307,55 @@ proteomics packages.")
 the graph algorithms contained in the Boost library.")
     (license license:artistic2.0)))
 
+(define-public r-rcas
+  (package
+    (name "r-rcas")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "RCAS" version))
+              (sha256
+               (base32
+                "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
+    (properties `((upstream-name . "RCAS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-cowplot" ,r-cowplot)
+       ("r-data-table" ,r-data-table)
+       ("r-dt" ,r-dt)
+       ("r-genomation" ,r-genomation)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicfeatures" ,r-genomicfeatures)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-ggseqlogo" ,r-ggseqlogo)
+       ("r-gprofiler2" ,r-gprofiler2)
+       ("r-iranges" ,r-iranges)
+       ("r-pbapply" ,r-pbapply)
+       ("r-pheatmap" ,r-pheatmap)
+       ("r-plotly" ,r-plotly)
+       ("r-plotrix" ,r-plotrix)
+       ("r-proxy" ,r-proxy)
+       ("r-ranger" ,r-ranger)
+       ("r-rsqlite" ,r-rsqlite)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-rmarkdown" ,r-rmarkdown)
+       ("r-s4vectors" ,r-s4vectors)
+       ("pandoc" ,pandoc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (synopsis "RNA-centric annotation system")
+    (description
+     "RCAS aims to be a standalone RNA-centric annotation system that provides
+intuitive reports and publication-ready graphics.  This package provides the R
+library implementing most of the pipeline's features.")
+    (home-page "https://github.com/BIMSBbioinfo/RCAS")
+    (license license:artistic2.0)))
+
 (define-public r-regioner
   (package
     (name "r-regioner")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ae61ecae74..a1ee4b6772 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7872,55 +7872,6 @@ including VCF header and contents in RDF and JSON.")
 secondary structure and comparative analysis in R.")
     (license license:gpl3+)))
 
-(define-public r-rcas
-  (package
-    (name "r-rcas")
-    (version "1.16.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "RCAS" version))
-              (sha256
-               (base32
-                "0vdxml618vqvf8xyh0zxs307p9zby0cj9dqyiiz625ilyq1hkw2m"))))
-    (properties `((upstream-name . "RCAS")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-data-table" ,r-data-table)
-       ("r-dt" ,r-dt)
-       ("r-genomation" ,r-genomation)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicfeatures" ,r-genomicfeatures)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-ggseqlogo" ,r-ggseqlogo)
-       ("r-gprofiler2" ,r-gprofiler2)
-       ("r-iranges" ,r-iranges)
-       ("r-pbapply" ,r-pbapply)
-       ("r-pheatmap" ,r-pheatmap)
-       ("r-plotly" ,r-plotly)
-       ("r-plotrix" ,r-plotrix)
-       ("r-proxy" ,r-proxy)
-       ("r-ranger" ,r-ranger)
-       ("r-rsqlite" ,r-rsqlite)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-rmarkdown" ,r-rmarkdown)
-       ("r-s4vectors" ,r-s4vectors)
-       ("pandoc" ,pandoc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (synopsis "RNA-centric annotation system")
-    (description
-     "RCAS aims to be a standalone RNA-centric annotation system that provides
-intuitive reports and publication-ready graphics.  This package provides the R
-library implementing most of the pipeline's features.")
-    (home-page "https://github.com/BIMSBbioinfo/RCAS")
-    (license license:artistic2.0)))
-
 (define-public rcas-web
   (package
     (name "rcas-web")
-- 
2.30.1

[bug#48575] [PATCH 42/50] gnu: r-mutationalpatterns: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Move from here...
* gnu/packages/bioconductor.scm (r-mutationalpatterns): ...to here.
---
 gnu/packages/bioconductor.scm   | 45 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 45 ---------------------------------
 2 files changed, 45 insertions(+), 45 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1d38fa1c05..7c471c7375 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3013,6 +3013,51 @@ different technologies, including microarrays, RNA-seq, and quantitative PCR.")
 throughput genetic sequencing data sets using regression methods.")
     (license license:artistic2.0)))
 
+(define-public r-mutationalpatterns
+  (package
+    (name "r-mutationalpatterns")
+    (version "3.0.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "MutationalPatterns" version))
+       (sha256
+        (base32
+         "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-biostrings" ,r-biostrings)
+       ("r-bsgenome" ,r-bsgenome)
+       ;; These two packages are suggested packages
+       ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
+       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
+       ("r-cowplot" ,r-cowplot)
+       ("r-dplyr" ,r-dplyr)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggalluvial" ,r-ggalluvial)
+       ("r-ggdendro" ,r-ggdendro)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-iranges" ,r-iranges)
+       ("r-magrittr" ,r-magrittr)
+       ("r-nmf" ,r-nmf)
+       ("r-pracma" ,r-pracma)
+       ("r-purrr" ,r-purrr)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-stringr" ,r-stringr)
+       ("r-tibble" ,r-tibble)
+       ("r-tidyr" ,r-tidyr)
+       ("r-variantannotation" ,r-variantannotation)))
+    (home-page "https://bioconductor.org/packages/MutationalPatterns/")
+    (synopsis "Extract and visualize mutational patterns in genomic data")
+    (description "This package provides an extensive toolset for the
+characterization and visualization of a wide range of mutational patterns
+in SNV base substitution data.")
+    (license license:expat)))
+
 (define-public r-msnbase
   (package
     (name "r-msnbase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a1ee4b6772..b5b2cc2f6b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7923,51 +7923,6 @@ secondary structure and comparative analysis in R.")
 @dfn{RNA-centric annotation system} (RCAS).")
     (license license:agpl3+)))
 
-(define-public r-mutationalpatterns
-  (package
-    (name "r-mutationalpatterns")
-    (version "3.0.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "MutationalPatterns" version))
-       (sha256
-        (base32
-         "1988kjjgq8af0hj7chhpxi88717wwmzs9qgrwapjh0hm2hjwhn35"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-biostrings" ,r-biostrings)
-       ("r-bsgenome" ,r-bsgenome)
-       ;; These two packages are suggested packages
-       ("r-bsgenome-hsapiens-1000g" ,r-bsgenome-hsapiens-1000genomes-hs37d5)
-       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
-       ("r-cowplot" ,r-cowplot)
-       ("r-dplyr" ,r-dplyr)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-ggalluvial" ,r-ggalluvial)
-       ("r-ggdendro" ,r-ggdendro)
-       ("r-ggplot2" ,r-ggplot2)
-       ("r-iranges" ,r-iranges)
-       ("r-magrittr" ,r-magrittr)
-       ("r-nmf" ,r-nmf)
-       ("r-pracma" ,r-pracma)
-       ("r-purrr" ,r-purrr)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-stringr" ,r-stringr)
-       ("r-tibble" ,r-tibble)
-       ("r-tidyr" ,r-tidyr)
-       ("r-variantannotation" ,r-variantannotation)))
-    (home-page "https://bioconductor.org/packages/MutationalPatterns/")
-    (synopsis "Extract and visualize mutational patterns in genomic data")
-    (description "This package provides an extensive toolset for the
-characterization and visualization of a wide range of mutational patterns
-in SNV base substitution data.")
-    (license license:expat)))
-
 (define-public r-chipkernels
   (let ((commit "c9cfcacb626b1221094fb3490ea7bac0fd625372")
         (revision "1"))
-- 
2.30.1

[bug#48575] [PATCH 43/50] gnu: r-tximport: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-tximport): Move from here...
* gnu/packages/bioconductor.scm (r-tximport): ...to here.
---
 gnu/packages/bioconductor.scm   | 24 ++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 24 ------------------------
 2 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7c471c7375..30d4844ae4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3848,6 +3848,30 @@ dependencies between GO terms can be implemented and applied.")
     ;; Any version of the LGPL applies.
     (license license:lgpl2.1+)))
 
+(define-public r-tximport
+  (package
+    (name "r-tximport")
+    (version "1.18.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "tximport" version))
+              (sha256
+               (base32
+                "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
+    (build-system r-build-system)
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/tximport")
+    (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
+    (description
+     "This package provides tools to import transcript-level abundance,
+estimated counts and transcript lengths, and to summarize them into matrices
+for use with downstream gene-level analysis packages.  Average transcript
+length, weighted by sample-specific transcript abundance estimates, is
+provided as a matrix which can be used as an offset for different expression
+of gene-level counts.")
+    (license license:gpl2+)))
+
 (define-public r-variantannotation
   (package
     (name "r-variantannotation")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b5b2cc2f6b..83d6797809 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,30 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
 factors bound at the specific regions.")
     (license license:gpl2+)))
 
-(define-public r-tximport
-  (package
-    (name "r-tximport")
-    (version "1.18.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "tximport" version))
-              (sha256
-               (base32
-                "1nxnlvl4iv2392xa72j0lzy2xnb3vrvyhfrdj9l54znwkrryyq34"))))
-    (build-system r-build-system)
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/tximport")
-    (synopsis "Import and summarize transcript-level estimates for gene-level analysis")
-    (description
-     "This package provides tools to import transcript-level abundance,
-estimated counts and transcript lengths, and to summarize them into matrices
-for use with downstream gene-level analysis packages.  Average transcript
-length, weighted by sample-specific transcript abundance estimates, is
-provided as a matrix which can be used as an offset for different expression
-of gene-level counts.")
-    (license license:gpl2+)))
-
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
-- 
2.30.1

[bug#48575] [PATCH 44/50] gnu: r-rhdf5filters: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rhdf5filters): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5filters): ...to here.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 26 --------------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 30d4844ae4..8695f13ed8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3482,6 +3482,32 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rhdf5filters
+  (package
+    (name "r-rhdf5filters")
+    (version "1.2.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "rhdf5filters" version))
+       (sha256
+        (base32
+         "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
+    (properties `((upstream-name . "rhdf5filters")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-rhdf5lib" ,r-rhdf5lib)))
+    (inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/grimbough/rhdf5filters")
+    (synopsis "HDF5 compression filters")
+    (description
+     "This package provides a collection of compression filters for use with
+HDF5 datasets.")
+    (license license:bsd-2)))
+
 (define-public r-rsamtools
   (package
     (name "r-rsamtools")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 83d6797809..2907d65b38 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,32 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
 factors bound at the specific regions.")
     (license license:gpl2+)))
 
-(define-public r-rhdf5filters
-  (package
-    (name "r-rhdf5filters")
-    (version "1.2.1")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "rhdf5filters" version))
-       (sha256
-        (base32
-         "1bjlgc76vx0z81s8vci9ln1d2s3b157qnm32xs36mnyjk31ivasz"))))
-    (properties `((upstream-name . "rhdf5filters")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-rhdf5lib" ,r-rhdf5lib)))
-    (inputs
-     `(("zlib" ,zlib)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/grimbough/rhdf5filters")
-    (synopsis "HDF5 compression filters")
-    (description
-     "This package provides a collection of compression filters for use with
-HDF5 datasets.")
-    (license license:bsd-2)))
-
 (define-public r-rhdf5
   (package
     (name "r-rhdf5")
-- 
2.30.1

[bug#48575] [PATCH 45/50] gnu: r-annotationfilter: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-annotationfilter): Move from here...
* gnu/packages/bioconductor.scm (r-annotationfilter): ...to here.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 26 --------------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 8695f13ed8..87b879ad94 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1804,6 +1804,32 @@ microarrays.")
 annotation data packages using SQLite data storage.")
     (license license:artistic2.0)))
 
+(define-public r-annotationfilter
+  (package
+    (name "r-annotationfilter")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "AnnotationFilter" version))
+              (sha256
+               (base32
+                "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
+    (properties
+     `((upstream-name . "AnnotationFilter")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-genomicranges" ,r-genomicranges)
+       ("r-lazyeval" ,r-lazyeval)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://github.com/Bioconductor/AnnotationFilter")
+    (synopsis "Facilities for filtering Bioconductor annotation resources")
+    (description
+     "This package provides classes and other infrastructure to implement
+filters for manipulating Bioconductor annotation resources.  The filters are
+used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
+    (license license:artistic2.0)))
+
 (define-public r-annotationforge
   (package
     (name "r-annotationforge")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2907d65b38..7ad51d3518 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8029,32 +8029,6 @@ package, and for letting R applications work on datasets that are larger than
 the available RAM.")
     (license license:artistic2.0)))
 
-(define-public r-annotationfilter
-  (package
-    (name "r-annotationfilter")
-    (version "1.14.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "AnnotationFilter" version))
-              (sha256
-               (base32
-                "0npk0laa2rc93rsh6yikj886zf2fl53a050j07fj9w67j0q0h3s9"))))
-    (properties
-     `((upstream-name . "AnnotationFilter")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-genomicranges" ,r-genomicranges)
-       ("r-lazyeval" ,r-lazyeval)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://github.com/Bioconductor/AnnotationFilter")
-    (synopsis "Facilities for filtering Bioconductor annotation resources")
-    (description
-     "This package provides classes and other infrastructure to implement
-filters for manipulating Bioconductor annotation resources.  The filters are
-used by @code{ensembldb}, @code{Organism.dplyr}, and other packages.")
-    (license license:artistic2.0)))
-
 (define-public emboss
   (package
     (name "emboss")
-- 
2.30.1

[bug#48575] [PATCH 46/50] gnu: r-rhdf5: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-rhdf5): Move from here...
* gnu/packages/bioconductor.scm (r-rhdf5): ...to here.
---
 gnu/packages/bioconductor.scm   | 39 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 39 ---------------------------------
 2 files changed, 39 insertions(+), 39 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 87b879ad94..d027a24bf3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3508,6 +3508,45 @@ reports together for a particular project that can be viewed in a web
 browser.")
     (license license:artistic2.0)))
 
+(define-public r-rhdf5
+  (package
+    (name "r-rhdf5")
+    (version "2.34.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "rhdf5" version))
+              (sha256
+               (base32
+                "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
+    (build-system r-build-system)
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         (add-after 'unpack 'fix-linking
+           (lambda _
+             (substitute* "src/Makevars"
+               ;; This is to avoid having a plain directory on the list of
+               ;; libraries to link.
+               (("\\(RHDF5_LIBS\\)" match)
+                (string-append match "/libhdf5.a")))
+             #t)))))
+    (propagated-inputs
+     `(("r-rhdf5filters" ,r-rhdf5filters)
+       ("r-rhdf5lib" ,r-rhdf5lib)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page "https://bioconductor.org/packages/rhdf5")
+    (synopsis "HDF5 interface to R")
+    (description
+     "This R/Bioconductor package provides an interface between HDF5 and R.
+HDF5's main features are the ability to store and access very large and/or
+complex datasets and a wide variety of metadata on mass storage (disk) through
+a completely portable file format.  The rhdf5 package is thus suited for the
+exchange of large and/or complex datasets between R and other software
+package, and for letting R applications work on datasets that are larger than
+the available RAM.")
+    (license license:artistic2.0)))
+
 (define-public r-rhdf5filters
   (package
     (name "r-rhdf5filters")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7ad51d3518..ef0d7b3007 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7990,45 +7990,6 @@ bound and non bound genomic regions to accurately identify transcription
 factors bound at the specific regions.")
     (license license:gpl2+)))
 
-(define-public r-rhdf5
-  (package
-    (name "r-rhdf5")
-    (version "2.34.0")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "rhdf5" version))
-              (sha256
-               (base32
-                "0almr1vscrgj5g4dyrags131wia2pmdbdidlpskbgm44ha6hpmqi"))))
-    (build-system r-build-system)
-    (arguments
-     `(#:phases
-       (modify-phases %standard-phases
-         (add-after 'unpack 'fix-linking
-           (lambda _
-             (substitute* "src/Makevars"
-               ;; This is to avoid having a plain directory on the list of
-               ;; libraries to link.
-               (("\\(RHDF5_LIBS\\)" match)
-                (string-append match "/libhdf5.a")))
-             #t)))))
-    (propagated-inputs
-     `(("r-rhdf5filters" ,r-rhdf5filters)
-       ("r-rhdf5lib" ,r-rhdf5lib)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr)))
-    (home-page "https://bioconductor.org/packages/rhdf5")
-    (synopsis "HDF5 interface to R")
-    (description
-     "This R/Bioconductor package provides an interface between HDF5 and R.
-HDF5's main features are the ability to store and access very large and/or
-complex datasets and a wide variety of metadata on mass storage (disk) through
-a completely portable file format.  The rhdf5 package is thus suited for the
-exchange of large and/or complex datasets between R and other software
-package, and for letting R applications work on datasets that are larger than
-the available RAM.")
-    (license license:artistic2.0)))
-
 (define-public emboss
   (package
     (name "emboss")
-- 
2.30.1

[bug#48575] [PATCH 47/50] gnu: r-chipseq: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-chipseq): Move from here...
* gnu/packages/bioconductor.scm (r-chipseq): ...to here.
---
 gnu/packages/bioconductor.scm   | 26 ++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 26 --------------------------
 2 files changed, 26 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index d027a24bf3..f224a5ecb4 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2206,6 +2206,32 @@ genome data packages and support for efficient SNP representation.")
 analysis.")
     (license license:artistic2.0)))
 
+(define-public r-chipseq
+  (package
+    (name "r-chipseq")
+    (version "1.40.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "chipseq" version))
+       (sha256
+        (base32
+         "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocgenerics" ,r-biocgenerics)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-iranges" ,r-iranges)
+       ("r-lattice" ,r-lattice)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-shortread" ,r-shortread)))
+    (home-page "https://bioconductor.org/packages/chipseq")
+    (synopsis "Package for analyzing ChIPseq data")
+    (description
+     "This package provides tools for processing short read data from ChIPseq
+experiments.")
+    (license license:artistic2.0)))
+
 (define-public r-complexheatmap
   (package
     (name "r-complexheatmap")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ef0d7b3007..3ee3d9d4f3 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
-(define-public r-chipseq
-  (package
-    (name "r-chipseq")
-    (version "1.40.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "chipseq" version))
-       (sha256
-        (base32
-         "12pzq24aarvgxfmhcad0l5g951xqdvvi7bspgbsvlvmfkqd74j2v"))))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocgenerics" ,r-biocgenerics)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-iranges" ,r-iranges)
-       ("r-lattice" ,r-lattice)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-shortread" ,r-shortread)))
-    (home-page "https://bioconductor.org/packages/chipseq")
-    (synopsis "Package for analyzing ChIPseq data")
-    (description
-     "This package provides tools for processing short read data from ChIPseq
-experiments.")
-    (license license:artistic2.0)))
-
 (define-public r-copyhelper
   (package
     (name "r-copyhelper")
-- 
2.30.1

[bug#48575] [PATCH 48/50] gnu: r-copyhelper: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-copyhelper): Move from here...
* gnu/packages/bioconductor.scm (r-copyhelper): ...to here.
[source]: Repalce 'string-append' by 'bioconductor-uri' with 'experiment.
---
 gnu/packages/bioconductor.scm   | 24 ++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 26 --------------------------
 2 files changed, 24 insertions(+), 26 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index f224a5ecb4..eee1561c1b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -999,6 +999,30 @@ from Illumina 450k methylation arrays.")
 chromstaR package.")
     (license license:gpl3)))
 
+(define-public r-copyhelper
+  (package
+    (name "r-copyhelper")
+    (version "1.6.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CopyhelpeR" version 'experiment))
+       (sha256
+        (base32
+         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
+    (properties `((upstream-name . "CopyhelpeR")))
+    (build-system r-build-system)
+    (home-page "https://bioconductor.org/packages/CopyhelpeR/")
+    (synopsis "Helper files for CopywriteR")
+    (description
+     "This package contains the helper files that are required to run the
+Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
+and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
+mm10.  In addition, it contains a blacklist filter to remove regions that
+display copy number variation.  Files are stored as GRanges objects from the
+GenomicRanges Bioconductor package.")
+    (license license:gpl2)))
+
 (define-public r-genelendatabase
   (package
     (name "r-genelendatabase")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 3ee3d9d4f3..2acca0c055 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,32 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
-(define-public r-copyhelper
-  (package
-    (name "r-copyhelper")
-    (version "1.6.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (string-append "https://bioconductor.org/packages/release/"
-                           "data/experiment/src/contrib/CopyhelpeR_"
-                           version ".tar.gz"))
-       (sha256
-        (base32
-         "0x7cyynjmxls9as2gg0iyp9x5fpalxmdjq914ss7i84i9zyk5bhq"))))
-    (properties `((upstream-name . "CopyhelpeR")))
-    (build-system r-build-system)
-    (home-page "https://bioconductor.org/packages/CopyhelpeR/")
-    (synopsis "Helper files for CopywriteR")
-    (description
-     "This package contains the helper files that are required to run the
-Bioconductor package CopywriteR.  It contains pre-assembled 1kb bin GC-content
-and mappability files for the reference genomes hg18, hg19, hg38, mm9 and
-mm10.  In addition, it contains a blacklist filter to remove regions that
-display copy number variation.  Files are stored as GRanges objects from the
-GenomicRanges Bioconductor package.")
-    (license license:gpl2)))
-
 (define-public r-copywriter
   (package
     (name "r-copywriter")
-- 
2.30.1

[bug#48575] [PATCH 49/50] gnu: r-copywriter: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-copywriter): Move from here...
* gnu/packages/bioconductor.scm (r-copywriter): ...to here.
---
 gnu/packages/bioconductor.scm   | 40 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 40 ---------------------------------
 2 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index eee1561c1b..fe91fd486f 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2295,6 +2295,46 @@ provides a highly flexible way to arrange multiple heatmaps and supports
 self-defined annotation graphics.")
     (license license:gpl2+)))
 
+(define-public r-copywriter
+  (package
+    (name "r-copywriter")
+    (version "2.22.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "CopywriteR" version))
+       (sha256
+        (base32
+         "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
+    (properties `((upstream-name . "CopywriteR")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biocparallel" ,r-biocparallel)
+       ("r-chipseq" ,r-chipseq)
+       ("r-copyhelper" ,r-copyhelper)
+       ("r-data-table" ,r-data-table)
+       ("r-dnacopy" ,r-dnacopy)
+       ("r-futile-logger" ,r-futile-logger)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-matrixstats" ,r-matrixstats)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-s4vectors" ,r-s4vectors)))
+    (home-page "https://github.com/PeeperLab/CopywriteR")
+    (synopsis "Copy number information from targeted sequencing")
+    (description
+     "CopywriteR extracts DNA copy number information from targeted sequencing
+by utilizing off-target reads.  It allows for extracting uniformly distributed
+copy number information, can be used without reference, and can be applied to
+sequencing data obtained from various techniques including chromatin
+immunoprecipitation and target enrichment on small gene panels.  Thereby,
+CopywriteR constitutes a widely applicable alternative to available copy
+number detection tools.")
+    (license license:gpl2)))
+
 (define-public r-deseq
   (package
     (name "r-deseq")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 2acca0c055..79146f915f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,46 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
-(define-public r-copywriter
-  (package
-    (name "r-copywriter")
-    (version "2.22.0")
-    (source
-     (origin
-       (method url-fetch)
-       (uri (bioconductor-uri "CopywriteR" version))
-       (sha256
-        (base32
-         "060p6l6l8i6b15hyyz5v5kkxih3h4wcciixii51m9mn82z23xr2f"))))
-    (properties `((upstream-name . "CopywriteR")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-biocparallel" ,r-biocparallel)
-       ("r-chipseq" ,r-chipseq)
-       ("r-copyhelper" ,r-copyhelper)
-       ("r-data-table" ,r-data-table)
-       ("r-dnacopy" ,r-dnacopy)
-       ("r-futile-logger" ,r-futile-logger)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicalignments" ,r-genomicalignments)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-matrixstats" ,r-matrixstats)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-s4vectors" ,r-s4vectors)))
-    (home-page "https://github.com/PeeperLab/CopywriteR")
-    (synopsis "Copy number information from targeted sequencing")
-    (description
-     "CopywriteR extracts DNA copy number information from targeted sequencing
-by utilizing off-target reads.  It allows for extracting uniformly distributed
-copy number information, can be used without reference, and can be applied to
-sequencing data obtained from various techniques including chromatin
-immunoprecipitation and target enrichment on small gene panels.  Thereby,
-CopywriteR constitutes a widely applicable alternative to available copy
-number detection tools.")
-    (license license:gpl2)))
-
 (define-public r-methylkit
   (package
     (name "r-methylkit")
-- 
2.30.1

[bug#48575] [PATCH 50/50] gnu: r-methylkit: Move to (gnu packages bioconductor).

[zimoun]

* gnu/packages/bioinformatics.scm (r-methylkit): Move from here...
* gnu/packages/bioconductor.scm (r-methylkit): ...to here.
---
 gnu/packages/bioconductor.scm   | 47 +++++++++++++++++++++++++++++++++
 gnu/packages/bioinformatics.scm | 47 ---------------------------------
 2 files changed, 47 insertions(+), 47 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index fe91fd486f..54a6afcf3d 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3102,6 +3102,53 @@ and the assessment of differential expression.  The analysis methods apply to
 different technologies, including microarrays, RNA-seq, and quantitative PCR.")
     (license license:gpl2+)))
 
+(define-public r-methylkit
+  (package
+    (name "r-methylkit")
+    (version "1.16.1")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "methylKit" version))
+              (sha256
+               (base32
+                "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
+    (properties `((upstream-name . "methylKit")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-data-table" ,r-data-table)
+       ("r-emdbook" ,r-emdbook)
+       ("r-fastseg" ,r-fastseg)
+       ("r-genomeinfodb" ,r-genomeinfodb)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-gtools" ,r-gtools)
+       ("r-iranges" ,r-iranges)
+       ("r-kernsmooth" ,r-kernsmooth)
+       ("r-limma" ,r-limma)
+       ("r-mclust" ,r-mclust)
+       ("r-mgcv" ,r-mgcv)
+       ("r-qvalue" ,r-qvalue)
+       ("r-r-utils" ,r-r-utils)
+       ("r-rcpp" ,r-rcpp)
+       ("r-rhtslib" ,r-rhtslib)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-s4vectors" ,r-s4vectors)
+       ("r-zlibbioc" ,r-zlibbioc)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr))) ; for vignettes
+    (home-page "https://github.com/al2na/methylKit")
+    (synopsis
+     "DNA methylation analysis from high-throughput bisulfite sequencing results")
+    (description
+     "MethylKit is an R package for DNA methylation analysis and annotation
+from high-throughput bisulfite sequencing.  The package is designed to deal
+with sequencing data from @dfn{Reduced representation bisulfite
+sequencing} (RRBS) and its variants, but also target-capture methods and whole
+genome bisulfite sequencing.  It also has functions to analyze base-pair
+resolution 5hmC data from experimental protocols such as oxBS-Seq and
+TAB-Seq.")
+    (license license:artistic2.0)))
+
 (define-public r-motifrg
   (package
     (name "r-motifrg")
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 79146f915f..48b521f755 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -8312,53 +8312,6 @@ analysis, variant tools is project based and provides a whole set of tools to
 manipulate and analyze genetic variants.")
     (license license:gpl3+)))
 
-(define-public r-methylkit
-  (package
-    (name "r-methylkit")
-    (version "1.16.1")
-    (source (origin
-              (method url-fetch)
-              (uri (bioconductor-uri "methylKit" version))
-              (sha256
-               (base32
-                "1c9b11gfh3cc37iwym9rgsba3mh2xkp78a1gvnjqhzlkiz667mn3"))))
-    (properties `((upstream-name . "methylKit")))
-    (build-system r-build-system)
-    (propagated-inputs
-     `(("r-data-table" ,r-data-table)
-       ("r-emdbook" ,r-emdbook)
-       ("r-fastseg" ,r-fastseg)
-       ("r-genomeinfodb" ,r-genomeinfodb)
-       ("r-genomicranges" ,r-genomicranges)
-       ("r-gtools" ,r-gtools)
-       ("r-iranges" ,r-iranges)
-       ("r-kernsmooth" ,r-kernsmooth)
-       ("r-limma" ,r-limma)
-       ("r-mclust" ,r-mclust)
-       ("r-mgcv" ,r-mgcv)
-       ("r-qvalue" ,r-qvalue)
-       ("r-r-utils" ,r-r-utils)
-       ("r-rcpp" ,r-rcpp)
-       ("r-rhtslib" ,r-rhtslib)
-       ("r-rsamtools" ,r-rsamtools)
-       ("r-rtracklayer" ,r-rtracklayer)
-       ("r-s4vectors" ,r-s4vectors)
-       ("r-zlibbioc" ,r-zlibbioc)))
-    (native-inputs
-     `(("r-knitr" ,r-knitr))) ; for vignettes
-    (home-page "https://github.com/al2na/methylKit")
-    (synopsis
-     "DNA methylation analysis from high-throughput bisulfite sequencing results")
-    (description
-     "MethylKit is an R package for DNA methylation analysis and annotation
-from high-throughput bisulfite sequencing.  The package is designed to deal
-with sequencing data from @dfn{Reduced representation bisulfite
-sequencing} (RRBS) and its variants, but also target-capture methods and whole
-genome bisulfite sequencing.  It also has functions to analyze base-pair
-resolution 5hmC data from experimental protocols such as oxBS-Seq and
-TAB-Seq.")
-    (license license:artistic2.0)))
-
 (define-public r-raremetals2
   (package
     (name "r-raremetals2")
-- 
2.30.1

bug#48575: [PATCH 00/50] Move some Bioconductor packages to (gnu packages bioconductor).

[Ricardo Wurmus]

Thank you for working on this!
I have just applied these patches.

-- 
Ricardo