[bug#59142] [PATCH] gnu: Add r-pals, r-glmnetutils and r-pando.

[bug#59142] [PATCH] gnu: Add r-pals, r-glmnetutils and r-pando.

[MadalinIonel.Patrascu]

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* gnu/packages/bioinformatics.scm (r-pando): New variable.

* gnu/packages/cran.scm (r-glmnetutils and r-pals): New variables.

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[bug#59142] [PATCH 1/3] gnu: Add r-pals.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index eff789ba8d..7f5ad1faf3 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -1661,6 +1661,31 @@ (define-public r-pacman
 functions which can speed up workflow.")
     (license license:gpl2)))
 
+(define-public r-pals
+  (package
+    (name "r-pals")
+    (version "1.7")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "pals" version))
+              (sha256
+               (base32
+                "18pbivmqs9yqsb6p8anv42alny0njaq3dajibhzysax0b7rsk2js"))))
+    (properties `((upstream-name . "pals")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-colorspace
+           r-dichromat
+           r-mapproj
+           r-maps))
+    (native-inputs (list r-knitr))
+    (home-page "https://kwstat.github.io/pals/")
+    (synopsis "Color palettes, color maps, and tools to evaluate them")
+    (description
+     "This package provides a comprehensive collection of color palettes, color
+maps, and tools to evaluate them.")
+    (license license:gpl3)))
+
 (define-public r-paralleldist
   (package
     (name "r-paralleldist")

base-commit: 7de6aa8a0abdb54727e1dd8f775802284b99e707
-- 
2.38.1

[bug#59142] [PATCH 2/3] gnu: Add r-glmnetutils.

[Mădălin Ionel Patrașcu]

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

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index 7f5ad1faf3..71843a8cb6 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -4153,6 +4153,32 @@ (define-public r-glue
 Docstrings (PEP-0257) and Julia's Triple-Quoted String Literals.")
     (license license:expat)))
 
+(define-public r-glmnetutils
+  (package
+    (name "r-glmnetutils")
+    (version "1.1.8")
+    (source (origin
+              (method url-fetch)
+              (uri (cran-uri "glmnetUtils" version))
+              (sha256
+               (base32
+                "1k8ivzjgpkm2a948qxx3wmkhlppbk31qc76spv2pscmp24x0lxyn"))))
+    (properties `((upstream-name . "glmnetUtils")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-glmnet
+           r-matrix))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hongooi73/glmnetUtils")
+    (synopsis
+     "Streamline the process of fitting elastic net models with glmnet")
+    (description
+     "This package provides a collection of tools to streamline the process of
+fitting elastic net models with @code{glmnet}.  In addition to providing a formula
+interface, it also features a function @code{cva.glmnet} to do crossvalidation
+for both α and λ, as well as some utility functions.")
+    (license license:gpl2)))
+
 (define-public r-paletteer
   (package
     (name "r-paletteer")
-- 
2.38.1

[bug#59142] [PATCH 3/3] gnu: Add r-pando.

[Mădălin Ionel Patrașcu]

* gnu/packages/bioinformatics.scm (r-pando): 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 47f5574eeb..87c93bab4d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7600,6 +7600,56 @@ (define-public r-chromunity
 Pore-C concatemers.")
       (license license:gpl3))))
 
+(define-public r-pando
+  (package
+    (name "r-pando")
+    (version "1.0.1")
+    (source
+     (origin
+       (method git-fetch)
+       (uri (git-reference
+            (url "https://github.com/quadbiolab/Pando")
+            (commit (string-append "v" version))))
+       (file-name (git-file-name name version))
+       (sha256
+        (base32 "0c83anzdrbvg47p9xns2bxpjlx5z328can3jmzilw6rygwp7hyii"))))
+    (properties `((upstream-name . "Pando")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-bayestestr
+           r-brms
+           r-foreach
+           r-genomicranges
+           r-ggplot2
+           r-ggpointdensity
+           r-ggraph
+           r-glmnetutils
+           r-iranges
+           r-irlba
+           r-matrix
+           r-motifmatchr
+           r-pals
+           r-patchwork
+           r-seurat
+           r-signac
+           r-sparsematrixstats
+           r-tfbstools
+           r-tidygraph
+           r-tidyverse
+           r-uwot
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/quadbiolab/Pando")
+    (synopsis
+     "Inferring regulomes from multi-modal single-cell genomics data")
+    (description
+     "@code{Pando} leverages multi-modal single-cell measurements to infer gene
+regulatory networks using a flexible linear model-based framework.  By modeling
+the relationship between TF-binding site pairs with the expression of target
+genes, @code{Pando} simultaneously infers gene modules and sets of regulatory
+regions for each transcription factor.")
+    (license license:expat)))
+
 (define-public r-presto
   (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
         (revision "0"))
-- 
2.38.1

bug#59142: [PATCH 1/3] gnu: Add r-pals.

[Ricardo Wurmus]

I applied this series with minor indentation changes.  Thank you!

-- 
Ricardo