[bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam.

[bug#58879] [PATCH] gnu: Add r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam.

[MadalinIonel.Patrascu]

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* gnu/packages/bioconductor.scm (r-deco, r-decomplexdisease, r-decomptumor2sig, r-deconrnaseq and r-decontam): New variables.


Unrelated patches, added in the alphabetical order.


All the best,

     Mădălin Ionel Patrașcu!

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[bug#58879] [PATCH 1/5] gnu: Add r-deco.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-deco): New variable.
---
 gnu/packages/bioconductor.scm | 42 +++++++++++++++++++++++++++++++++++
 1 file changed, 42 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index b8535250f9..2f2268e5e6 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3075,6 +3075,48 @@ (define-public r-decipher
 biological sequences.")
     (license license:gpl3)))
 
+(define-public r-deco
+  (package
+    (name "r-deco")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "deco" version))
+              (sha256
+               (base32
+                "18n5zgln33c79jbjzjlivs8ihyg8zci6minfqlvagxgzcpa67k0m"))))
+    (properties `((upstream-name . "deco")))
+    (build-system r-build-system)
+    (propagated-inputs
+      (list r-ade4
+            r-annotationdbi
+            r-biobase
+            r-biocparallel
+            r-biocstyle
+            r-cluster
+            r-foreign
+            r-gdata
+            r-ggplot2
+            r-gplots
+            r-gridextra
+            r-limma
+            r-locfit
+            r-made4
+            r-rcolorbrewer
+            r-reshape2
+            r-scatterplot3d
+            r-sfsmisc
+            r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/fjcamlab/deco")
+    (synopsis "Decomposing heterogeneous cohorts using omic data profiling")
+    (description
+     "The package discovers differential features in hetero- and homogeneous omic
+data by a two-step method including subsampling @code{LIMMA} and @code{NSCA}.
+@code{DECO} reveals feature associations to hidden subclasses not exclusively
+related to higher deregulation levels.")
+    (license (license:fsdg-compatible "GPL (>=3)"))))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")

base-commit: ac51b9c86d58cfdb13ee643a2fdc8e979939a260
-- 
2.38.0

[bug#58879] [PATCH 2/5] gnu: Add r-decomplexdisease.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-decomplexdisease): New variable.
---
 gnu/packages/bioconductor.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 2f2268e5e6..809ba69bc3 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3117,6 +3117,39 @@ (define-public r-deco
 related to higher deregulation levels.")
     (license (license:fsdg-compatible "GPL (>=3)"))))
 
+(define-public r-decomplexdisease
+  (package
+    (name "r-decomplexdisease")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DEComplexDisease" version))
+              (sha256
+               (base32
+                "09a967x1rnv7byjwh29ngjhs67rgg27zblmlzx6pyqlwy5jsp89d"))))
+    (properties `((upstream-name . "DEComplexDisease")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-complexheatmap
+           r-deseq2
+           r-edger
+           r-rcpp
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/DEComplexDisease")
+    (synopsis "Investigations of complex diseases by bi-clustering analysis")
+    (description
+     "@code{DEComplexDisease} is designed to find the @acronym{DEGs, Differential
+Expressed Genes} for complex disease, which is characterized by the heterogeneous
+genomic expression profiles.  Different from the established DEG analysis tools,
+it does not assume the patients of complex diseases to share the common DEGs.
+By applying a bi-clustering algorithm, @code{DEComplexDisease} finds the DEGs
+shared by as many patients.  Applying the @code{DEComplexDisease} analysis
+results, users are possible to find the patients affected by the same mechanism
+based on the shared signatures.")
+    (license license:gpl3)))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-- 
2.38.0

[bug#58879] [PATCH 3/5] gnu: Add r-decomptumor2sig.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-decomptumor2sig): New variable.
---
 gnu/packages/bioconductor.scm | 43 +++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 809ba69bc3..7f6ba37bf8 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3150,6 +3150,49 @@ (define-public r-decomplexdisease
 based on the shared signatures.")
     (license license:gpl3)))
 
+(define-public r-decomptumor2sig
+  (package
+    (name "r-decomptumor2sig")
+    (version "2.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "decompTumor2Sig" version))
+              (sha256
+               (base32
+                "04hg9bbga2s8scjxfd8wjlmr45nzzvh8d6gr0w929sybx4nj2qz6"))))
+    (properties `((upstream-name . "decompTumor2Sig")))
+    (build-system r-build-system)
+    (inputs (list perl)) ;script/extractSpecColumns.pl
+    (propagated-inputs
+     (list r-biocgenerics
+           r-biostrings
+           r-bsgenome-hsapiens-ucsc-hg19
+           r-data-table
+           r-genomeinfodb
+           r-genomicfeatures
+           r-genomicranges
+           r-ggplot2
+           r-ggseqlogo
+           r-gridextra
+           r-matrix
+           r-plyr
+           r-quadprog
+           r-readxl
+           r-s4vectors
+           r-summarizedexperiment
+           r-txdb-hsapiens-ucsc-hg19-knowngene
+           r-variantannotation))
+    (native-inputs (list r-knitr))
+    (home-page "https://rmpiro.net/decompTumor2Sig/")
+    (synopsis "Decomposition of individual tumors into mutational signatures")
+    (description
+     "The package uses quadratic programming for signature refitting, i.e., to
+decompose the mutation catalog from an individual tumor sample into a set of given
+mutational signatures (either Alexandrov-model signatures or Shiraishi-model
+signatures), computing weights that reflect the contributions of the signatures
+to the mutation load of the tumor.")
+    (license license:gpl2)))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-- 
2.38.0

[bug#58879] [PATCH 4/5] gnu: Add r-deconrnaseq.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-deconrnaseq): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 7f6ba37bf8..ce95a9e5af 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3193,6 +3193,33 @@ (define-public r-decomptumor2sig
 to the mutation load of the tumor.")
     (license license:gpl2)))
 
+(define-public r-deconrnaseq
+  (package
+    (name "r-deconrnaseq")
+    (version "1.38.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "DeconRNASeq" version))
+              (sha256
+               (base32
+                "10smk88srxm58hli0fhkdfd6l5z02q58xc9mww39gkn71y0127k6"))))
+    (properties `((upstream-name . "DeconRNASeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-limsolve
+           r-pcamethods))
+    (home-page "https://bioconductor.org/packages/DeconRNASeq")
+    (synopsis
+     "Deconvolution of heterogeneous tissue samples for mRNA-Seq data")
+    (description
+     "@code{DeconSeq} is an R package for deconvolution of heterogeneous tissues
+based on mRNA-Seq data.  It models the expression levels from heterogeneous cell
+populations in mRNA-Seq as the weighted average of expression from different
+constituting cell types and predicted cell type proportions of single expression
+profiles.")
+    (license license:gpl2)))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-- 
2.38.0

[bug#58879] [PATCH 5/5] gnu: Add r-decontam.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioconductor.scm (r-decontam): New variable.
---
 gnu/packages/bioconductor.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index ce95a9e5af..e1175e46f1 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -3220,6 +3220,33 @@ (define-public r-deconrnaseq
 profiles.")
     (license license:gpl2)))
 
+(define-public r-decontam
+  (package
+    (name "r-decontam")
+    (version "1.16.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "decontam" version))
+              (sha256
+               (base32
+                "1g9hcfcfnpq6z21069yw0pyzncwznmvxb2xalg4y6y1604dy98q9"))))
+    (properties `((upstream-name . "decontam")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2
+           r-reshape2))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/benjjneb/decontam")
+    (synopsis
+     "Identification of the contaminants in marker-gene and metagenomics data")
+    (description
+     "This package offers simple statistical identification of contaminating
+sequence features in marker-gene or metagenomics data.  Works on any kind of
+feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic
+groups, MAGs,...).  Requires DNA quantitation data or sequenced negative control
+samples.")
+    (license license:artistic2.0)))
+
 (define-public r-deconvr
   (package
     (name "r-deconvr")
-- 
2.38.0

bug#58879: [PATCH 1/5] gnu: Add r-deco.

[Ricardo Wurmus]

Applied all with minor changes (indentation, license, description).

Thanks!

-- 
Ricardo