[bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix.

[bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-bumpymatrix): 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 74071900a3..6204173277 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -12913,6 +12913,33 @@ (define-public r-siggenes
 Bayes Analyses of Microarrays} (EBAM).")
     (license license:lgpl2.0+)))
 
+(define-public r-bumpymatrix
+  (package
+    (name "r-bumpymatrix")
+    (version "1.8.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BumpyMatrix" version))
+              (sha256
+               (base32
+                "021xn5d08phmwv6g8a5d4ap5kcf5syhm6vpr784l4k54lflssr5i"))))
+    (properties `((upstream-name . "BumpyMatrix")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-iranges r-matrix r-s4vectors))
+    (native-inputs (list r-knitr))
+    (home-page "https://bioconductor.org/packages/BumpyMatrix")
+    (synopsis "Bumpy matrix of non-scalar objects")
+    (description
+     "
+@code{BumpyMatrix} class and subclasses for storing non-scalar objects in matrix entries.
+This is akin to a ragged array but the raggedness is in the third dimension,
+much like a bumpy surface - hence the name.  Of particular interest is the
+@code{BumpyDataFrameMatrix,} where each entry is a Bioconductor data frame.
+This allows us to naturally represent multivariate data in a format that is
+compatible with two-dimensional containers like the @code{SummarizedExperiment}
+and @code{MultiAssayExperiment} objects.")
+    (license license:expat)))
+
 (define-public r-bumphunter
   (package
     (name "r-bumphunter")

base-commit: 39fa1ef033fda82cb1d122e0d1675b51acb1db34
-- 
2.34.1

[bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata.

[Navid Afkhami]

* gnu/packages/bioconductor.scm (r-mousegastrulationdata): New variable.
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 6204173277..f3671e5cca 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -8009,6 +8009,37 @@ (define-public r-motifrg
 throughput genetic sequencing data sets using regression methods.")
     (license license:artistic2.0)))
 
+(define-public r-mousegastrulationdata
+  (package
+    (name "r-mousegastrulationdata")
+    (version "1.14.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "MouseGastrulationData" version
+                                     'experiment))
+              (sha256
+               (base32
+                "155kci5isq7mlbvv8mdl2jjpafm3pbv1likhls70aa746spr1h17"))))
+    (properties `((upstream-name . "MouseGastrulationData")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-biocgenerics
+                             r-bumpymatrix
+                             r-experimenthub
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-spatialexperiment
+                             r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/MarioniLab/MouseGastrulationData")
+    (synopsis
+     "Single-Cell omics data across mouse gastrulation and early organogenesis")
+    (description
+     "This package provides processed and raw count data for single-cell RNA sequencing.
+in addition, this package offers single-cell ATAC-seq, and @code{seqFISH}
+(spatial transcriptomic) experiments performed along a timecourse of mouse
+gastrulation and early organogenesis.")
+    (license license:gpl3)))
+
 (define-public r-muscat
   (package
     (name "r-muscat")
-- 
2.34.1

bug#65499: [PATCH 1/2] gnu: Add r-bumpymatrix.

[Ricardo Wurmus]

Applied with minor changes.  Thanks!

-- 
Ricardo

bug#65500: [PATCH 2/2] gnu: Add r-mousegastrulationdata.

[Ricardo Wurmus]

Applied with minor changes:

- location in the file, next to other experiment packages
- formatting of the description.

-- 
Ricardo