* [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix.
@ 2023-08-24 13:28 Navid Afkhami
2023-08-24 13:28 ` [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata Navid Afkhami
2023-08-28 8:20 ` bug#65499: [PATCH 1/2] gnu: Add r-bumpymatrix Ricardo Wurmus
0 siblings, 2 replies; 4+ messages in thread
From: Navid Afkhami @ 2023-08-24 13:28 UTC (permalink / raw)
To: 65499; +Cc: 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata.
2023-08-24 13:28 [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix Navid Afkhami
@ 2023-08-24 13:28 ` Navid Afkhami
2023-08-28 8:20 ` bug#65500: " Ricardo Wurmus
2023-08-28 8:20 ` bug#65499: [PATCH 1/2] gnu: Add r-bumpymatrix Ricardo Wurmus
1 sibling, 1 reply; 4+ messages in thread
From: Navid Afkhami @ 2023-08-24 13:28 UTC (permalink / raw)
To: 65500; +Cc: 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* bug#65499: [PATCH 1/2] gnu: Add r-bumpymatrix.
2023-08-24 13:28 [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix Navid Afkhami
2023-08-24 13:28 ` [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata Navid Afkhami
@ 2023-08-28 8:20 ` Ricardo Wurmus
1 sibling, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2023-08-28 8:20 UTC (permalink / raw)
To: 65499-done
Applied with minor changes. Thanks!
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
* bug#65500: [PATCH 2/2] gnu: Add r-mousegastrulationdata.
2023-08-24 13:28 ` [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata Navid Afkhami
@ 2023-08-28 8:20 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2023-08-28 8:20 UTC (permalink / raw)
To: 65500-done
Applied with minor changes:
- location in the file, next to other experiment packages
- formatting of the description.
--
Ricardo
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2023-08-28 8:22 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2023-08-24 13:28 [bug#65499] [PATCH 1/2] gnu: Add r-bumpymatrix Navid Afkhami
2023-08-24 13:28 ` [bug#65500] [PATCH 2/2] gnu: Add r-mousegastrulationdata Navid Afkhami
2023-08-28 8:20 ` bug#65500: " Ricardo Wurmus
2023-08-28 8:20 ` bug#65499: [PATCH 1/2] gnu: Add r-bumpymatrix Ricardo Wurmus
Code repositories for project(s) associated with this external index
https://git.savannah.gnu.org/cgit/guix.git
This is an external index of several public inboxes,
see mirroring instructions on how to clone and mirror
all data and code used by this external index.