[bug#53349] [PATCH 0/9] Add 2 bioinformatics R packages

[bug#53349] [PATCH 0/9] Add 2 bioinformatics R packages

[zimoun]

Hi,

This series adds two bioinformatics R packages and the missing dependencies.


zimoun (9):
  gnu: r-org-dr-eg-db: Update to 3.14.0.
  gnu: Add r-jetset.
  gnu: Add r-hgu133plus2-db.
  gnu: Add r-chorddiag.
  gnu: Add r-scico.
  gnu: Add r-add2ggplot.
  gnu: Add r-rlist.
  gnu: Add r-icellnet.
  gnu: Add r-scseqcomm.

 gnu/packages/bioconductor.scm   | 53 ++++++++++++++++--
 gnu/packages/bioinformatics.scm | 96 ++++++++++++++++++++++++++++++++-
 gnu/packages/cran.scm           | 69 +++++++++++++++++++++++-
 gnu/packages/statistics.scm     | 30 +++++++++++
 4 files changed, 243 insertions(+), 5 deletions(-)


base-commit: 5ed33b0d05902de921e972d41168910107c93515
-- 
2.34.0

[bug#53349] [PATCH 1/9] gnu: r-org-dr-eg-db: Update to 3.14.0.

[zimoun]

* gnu/packages/bioconductor.scm (r-org-dr-eg-db): Update to 3.14.0.
---
 gnu/packages/bioconductor.scm | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0fbe0965c2..7194e8b0e7 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5,7 +5,7 @@
 ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
 ;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
-;;; Copyright © 2019, 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
 ;;; Copyright © 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
 ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net>
@@ -626,13 +626,13 @@ (define-public r-org-dr-eg-db
 (define-public r-org-hs-eg-db
   (package
     (name "r-org-hs-eg-db")
-    (version "3.7.0")
+    (version "3.14.0")
     (source (origin
               (method url-fetch)
               (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation))
               (sha256
                (base32
-                "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim"))))
+                "0mnddv42ll0sc0zxf7hkgilslykbvfn7xgxg1g8qi57q2dmpwb6j"))))
     (properties
      `((upstream-name . "org.Hs.eg.db")))
     (build-system r-build-system)
-- 
2.34.0

[bug#53349] [PATCH 2/9] gnu: Add r-jetset.

[zimoun]

* gnu/packages/bioconductor.scm (r-jetset): 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 7194e8b0e7..935c958cd0 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1965,6 +1965,33 @@ (define-public r-deconstructsigs
 closely reconstructs the mutational profile.")
     (license license:gpl2+)))
 
+;; This is a CRAN package, but it depends on Bioconductor packages.
+(define-public r-jetset
+  (package
+    (name "r-jetset")
+    (version "3.4.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "jetset" version))
+       (sha256
+        (base32 "0c99h5npsv2gf5d59s4qhkaqmjhbwa3prcykk24wzhnpfq6y6xhp"))))
+    (properties `((upstream-name . "jetset")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+    (home-page "http://www.cbs.dtu.dk/biotools/jetset/")
+    (synopsis "One-to-one gene-probeset mapping for Affymetrix human microarrays")
+    (description
+     "This package provides a one-to-one mapping from gene to \"best\" probe
+set for four Affymetrix human gene expression microarrays: hgu95av2, hgu133a,
+hgu133plus2, and u133x3p.  On Affymetrix gene expression microarrays, a single
+gene may be measured by multiple probe sets.  This can present a mild
+conundrum when attempting to evaluate a gene \"signature\" that is defined by
+gene names rather than by specific probe sets.  This package also includes the
+pre-calculated probe set quality scores that were used to define the
+mapping.")
+    (license license:artistic2.0)))
+
 ;; This is a CRAN package, but it depends on Bioconductor packages.
 (define-public r-nmf
   (package
-- 
2.34.0

[bug#53349] [PATCH 3/9] gnu: Add r-hgu133plus2-db.

[zimoun]

* gnu/packages/bioconductor.scm (r-hgu133plus2-db): New variable.
---
 gnu/packages/bioconductor.scm | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 935c958cd0..aece88ab5b 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -956,6 +956,26 @@ (define-public r-do-db
 Disease Ontology.")
     (license license:artistic2.0)))
 
+(define-public r-hgu133plus2-db
+  (package
+    (name "r-hgu133plus2-db")
+    (version "3.13.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "hgu133plus2.db" version 'annotation))
+       (sha256
+        (base32 "0i6cfk7ahql4fcgrq0dai9gkjbsahyzd9iv4lqv1ad58fzkmipnx"))))
+    (properties `((upstream-name . "hgu133plus2.db")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-annotationdbi r-org-hs-eg-db))
+    (home-page "https://bioconductor.org/packages/hgu133plus2.db")
+    (synopsis "Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data")
+    (description
+     "This package provides Affymetrix HG-U133_Plus_2 array annotation
+data (chip hgu133plus2) assembled using data from public repositories.")
+    (license license:artistic2.0)))
+
 (define-public r-pfam-db
   (package
     (name "r-pfam-db")
-- 
2.34.0

[bug#53349] [PATCH 4/9] gnu: Add r-chorddiag.

[zimoun]

* gnu/packages/statistics.scm (r-chorddiag): New variable.
---
 gnu/packages/statistics.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/statistics.scm b/gnu/packages/statistics.scm
index f777ddf332..7fc1de6cc5 100644
--- a/gnu/packages/statistics.scm
+++ b/gnu/packages/statistics.scm
@@ -16,6 +16,7 @@
 ;;; Copyright © 2021 Bonface Munyoki Kilyungi <me@bonfacemunyoki.com>
 ;;; Copyright © 2021 Lars-Dominik Braun <lars@6xq.net>
 ;;; Copyright © 2021 Frank Pursel <frank.pursel@gmail.com>
+;;; Copyright © 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;;
 ;;; This file is part of GNU Guix.
 ;;;
@@ -847,6 +848,35 @@ (define-public r-bit64
 caching.")
     (license license:gpl2)))
 
+(define-public r-chorddiag
+  (package
+    (name "r-chorddiag")
+    (version "0.1.3")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+             (url "https://github.com/mattflor/chorddiag")
+             (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32
+         "1bpy9q861l1hyyiqbx2f7qzp7j7im8bkcfdwgxzk5fm0250p359a"))))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-htmlwidgets r-rcolorbrewer))
+    (native-inputs
+     (list r-knitr))
+    (home-page "https://github.com/mattflor/chorddiag")
+    (synopsis "Create D3 chord diagram")
+    (description
+     "This package provides tools to create interactive chords diagrams via
+the D3 Javascript library.  Chord diagrams show directed relationships among a
+group of entities.  This package is based on
+@url{http://bl.ocks.org/mbostock/4062006} with some modifications (fading) and
+additions (tooltips, bipartite diagram type).")
+    (license license:gpl3+)))
+
 (define-public r-dichromat
   (package
     (name "r-dichromat")
-- 
2.34.0

[bug#53349] [PATCH 5/9] gnu: Add r-scico.

[zimoun]

* gnu/packages/cran.scm (r-scico): New variable.
---
 gnu/packages/cran.scm | 26 +++++++++++++++++++++++++-
 1 file changed, 25 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ce7655e6a6..2caa12031b 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -31,7 +31,7 @@
 ;;; Copyright © 2020 Antoine Côté <antoine.cote@posteo.net>
 ;;; Copyright © 2020 Arun Isaac <arunisaac@systemreboot.net>
 ;;; Copyright © 2020 Magali Lemes <magalilemes00@gmail.com>
-;;; Copyright © 2020, 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2020 Aniket Patil <aniket112.patil@gmail.com>
 ;;; Copyright © 2021 Marcel Schilling <marcel.schilling@uni-luebeck.de>
 ;;; Copyright © 2021 Guillaume Le Vaillant <glv@posteo.net>
@@ -27108,6 +27108,30 @@ (define-public r-warp
 observations.")
     (license license:expat)))
 
+(define-public r-scico
+  (package
+    (name "r-scico")
+    (version "1.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "scico" version))
+       (sha256
+        (base32 "08grfbjd5s0vdw76ni37yjl2242rr8i2jy72sgpwgra282hpnji3"))))
+    (properties `((upstream-name . "scico")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-scales))
+    (home-page "https://github.com/thomasp85/scico")
+    (synopsis "Colour Palettes Based on the Scientific Colour-Maps")
+    (description
+     "This package provides colour choice in information visualisation.  It
+important in order to avoid being mislead by inherent bias in the used colour
+palette.  This package provides access to the perceptually uniform and
+colour-blindness friendly palettes developed by Fabio Crameri and released
+under the \"Scientific Colour-Maps\" moniker.  The package contains 24
+different palettes and includes both diverging and sequential types.")
+    (license license:expat)))
+
 (define-public r-slider
   (package
     (name "r-slider")
-- 
2.34.0

[bug#53349] [PATCH 6/9] gnu: Add r-add2ggplot.

[zimoun]

* gnu/packages/cran.scm (r-add2ggplot): New variable.
---
 gnu/packages/cran.scm | 21 +++++++++++++++++++++
 1 file changed, 21 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 2caa12031b..350ece7d35 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -26910,6 +26910,27 @@ (define-public r-adaptivesparsity
 geometric models.")
     (license license:lgpl3+)))
 
+(define-public r-add2ggplot
+  (package
+    (name "r-add2ggplot")
+    (version "0.3.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "add2ggplot" version))
+       (sha256
+        (base32 "0c94i1cfp2pvplvxmfvvz2fyj026r1jnax05mrzrc7ppnqzy25y0"))))
+    (properties `((upstream-name . "add2ggplot")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-ggplot2 r-magick r-magrittr r-rcolorbrewer r-zeallot))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/JiaxiangBU/add2ggplot")
+    (synopsis "Extension for ggplot2")
+    (description "This packages provides tools to create themes and color
+palettes for the package ggplot2.")
+    (license license:expat)))
+
 (define-public r-diffusionmap
   (package
     (name "r-diffusionmap")
-- 
2.34.0

[bug#53349] [PATCH 7/9] gnu: Add r-rlist.

[zimoun]

* gnu/packages/cran.scm (r-rlist): New variable.
---
 gnu/packages/cran.scm | 22 ++++++++++++++++++++++
 1 file changed, 22 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 350ece7d35..cb64c93f3e 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -27178,6 +27178,28 @@ (define-public r-slider
 sliding windows are to be created.")
     (license license:expat)))
 
+(define-public r-rlist
+  (package
+    (name "r-rlist")
+    (version "0.4.6.2")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (cran-uri "rlist" version))
+       (sha256
+        (base32 "15q99rhbbjq8zd976yjmfnny45dd5fg2p2dv1sljg2kwi66nbppb"))))
+    (properties `((upstream-name . "rlist")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-data-table r-jsonlite r-xml r-yaml))
+    (home-page "https://renkun-ken.github.io/rlist/")
+    (synopsis "A Toolbox for Non-Tabular Data Manipulation")
+    (description
+     "This package provides a set of functions for data manipulation with
+list objects, including mapping, filtering, grouping, sorting, updating,
+searching, and other useful functions.  Most functions are designed to be
+pipeline friendly so that data processing with lists can be chained.")
+    (license license:expat)))
+
 (define-public r-rsample
   (package
     (name "r-rsample")
-- 
2.34.0

[bug#53349] [PATCH 8/9] gnu: Add r-icellnet.

[zimoun]

* gnu/packages/bioinformatics.scm (r-icellnet): New variable.
---
 gnu/packages/bioinformatics.scm | 46 ++++++++++++++++++++++++++++++++-
 1 file changed, 45 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 6caeec80f7..b2bd7fbbc0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -21,7 +21,7 @@
 ;;; Copyright © 2020 Bonface Munyoki Kilyungi <bonfacemunyoki@gmail.com>
 ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com>
 ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de>
-;;; Copyright © 2021 Simon Tournier <zimon.toutoune@gmail.com>
+;;; Copyright © 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
 ;;; Copyright © 2021 Felix Gruber <felgru@posteo.net>
 ;;;
 ;;; This file is part of GNU Guix.
@@ -7771,6 +7771,50 @@ (define-public r-archr
        "This package is designed to streamline scATAC analyses in R.")
       (license license:gpl2+))))
 
+(define-public r-icellnet
+  ;; v1.0 tagged in 2020, last commit contains many fixes.
+  ;; DESCRIPTION says Version: 0.0.0.9000.
+  (let ((commit "b9c05488fb8b5ea69bd560018966eaf4e25f82a")
+        (revision "0"))
+    (package
+      (name "r-icellnet")
+      (version (git-version "1.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/soumelis-lab/ICELLNET")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "0cld7d6xqnvd0zpcpg3sx73an6vdc9divzywgnn6zxnqcd987cnw"))))
+      (build-system r-build-system)
+      (arguments
+       `(#:phases
+         (modify-phases %standard-phases
+           (add-after 'unpack 'enter-dir
+             (lambda _ (chdir "icellnet"))))))
+      (propagated-inputs
+       (list r-annotationdbi
+             r-data-table
+             r-dplyr
+             r-ggplot2
+             r-hgu133plus2-db
+             r-jetset
+             r-psych
+             r-reshape2
+             r-rlist))
+      (home-page "https://github.com/soumelis-lab/ICELLNET")
+      (synopsis "Transcriptomic-based framework to dissect cell communication")
+      (description "This packages provides a a transcriptomic-based framework
+to dissect cell communication in a global manner.  It integrates an original
+expert-curated database of ligand-receptor interactions taking into account
+multiple subunits expression.  Based on transcriptomic profiles (gene
+expression), this package allows to compute communication scores between cells
+and provides several visualization modes that can be helpful to dig into
+cell-cell interaction mechanism and extend biological knowledge.")
+      (license license:gpl3))))
+
 (define-public r-scde
   (package
     (name "r-scde")
-- 
2.34.0

[bug#53349] [PATCH 9/9] gnu: Add r-scseqcomm.

[zimoun]

* gnu/packages/bioinformatics.scm (r-scseqcomm): New variable.
---
 gnu/packages/bioinformatics.scm | 50 +++++++++++++++++++++++++++++++++
 1 file changed, 50 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index b2bd7fbbc0..6e7974e2d7 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7893,6 +7893,56 @@ (define-public r-misha
 analyze genomic data resulting from various experiments.")
     (license license:gpl2)))
 
+(define-public r-scseqcomm
+  (let ((commit "01076e703999f1a5aa76419d821b50aebe2b777a")
+        (revision "0"))
+    (package
+      (name "r-scseqcomm")
+      (version (git-version "0" revision commit))
+      (source
+       (origin
+         (method git-fetch)
+         (uri (git-reference
+               (url "https://gitlab.com/sysbiobig/scseqcomm")
+               (commit commit)))
+         (file-name (git-file-name name version))
+         (sha256
+          (base32
+           "1fw5si47d6agnz5fibmp2b1sv08pbpwv1j71w57xbav9044i032q"))
+         ;; Delete bundled dependency.
+         (modules '((guix build utils)))
+         (snippet
+          '(delete-file-recursively "other_deps"))))
+      (build-system r-build-system)
+      (inputs
+       (list r-add2ggplot
+             r-chorddiag
+             r-doparallel
+             r-dplyr
+             r-foreach
+             ;;r-grid ;; listed in DESCRIPTION
+             r-gridextra
+             r-ggplot2
+             r-gtable
+             r-htmlwidgets
+             r-igraph
+             r-matrix
+             ;;r-methods ;; listed in DESCRIPTION
+             r-org-hs-eg-db
+             r-psych
+             r-rcolorbrewer
+             r-rlang
+             r-scico
+             r-tidygraph
+             r-topgo))
+      (native-inputs
+       (list r-knitr))
+      (home-page "https://gitlab.com/sysbiobig/scseqcomm")
+      (synopsis "Inter- and intra- cellular signaling from single cell RNA-seq")
+      (description "This package is tools for analysing intercellular and
+intracellular signaling from single cell RNA-seq (scRNA-seq) data.")
+      (license license:gpl3))))
+
 (define-public r-shaman
   (let ((commit "d6944e8ac7bd1dbd5c6cec646eafc1d19d0ca96f")
         (release "2.0")
-- 
2.34.0

bug#53349: [PATCH 0/9] Add 2 bioinformatics R packages

[Ricardo Wurmus]

Hi,

thanks for the patches!

> zimoun (9):
>   gnu: r-org-dr-eg-db: Update to 3.14.0.
>   gnu: Add r-jetset.
>   gnu: Add r-hgu133plus2-db.
>   gnu: Add r-chorddiag.

This one contains minified JavaScript.  It’s only d3.js, so
it wasn’t hard to take the sources and minify it.

>   gnu: Add r-scico.
>   gnu: Add r-add2ggplot.
>   gnu: Add r-rlist.
>   gnu: Add r-icellnet.
>   gnu: Add r-scseqcomm.

I pushed them all to the master branch
(ce291b193cadbd6926ddf31af2ac6ed8bd607f44).

-- 
Ricardo

[bug#53349] [PATCH 0/9] Add 2 bioinformatics R packages

[zimoun]

Hi Ricardo,

On Fri, 21 Jan 2022 at 15:55, Ricardo Wurmus <rekado@elephly.net> wrote:

> >   gnu: Add r-chorddiag.
>
> This one contains minified JavaScript.  It’s only d3.js, so
> it wasn’t hard to take the sources and minify it.

Ah sorry.  Thanks for catching!

> I pushed them all to the master branch
> (ce291b193cadbd6926ddf31af2ac6ed8bd607f44).

Thanks,
simon