* [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#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
* 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
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.