* [bug#70536] [PATCH 2/2] v2 gnu: Add r-seraster.
@ 2024-04-23 14:23 14% ` Mădălin Ionel Patrașcu
0 siblings, 0 replies; 2+ results
From: Mădălin Ionel Patrașcu @ 2024-04-23 14:23 UTC (permalink / raw)
To: 70536
* gnu/packages/bioinformatics.scm (r-seraster): New variable.
Change-Id: I9f9fd24a9aa563f7c74154e613b85dee46bdcf79
---
gnu/packages/bioinformatics.scm | 39 +++++++++++++++++++++++++++++++++
1 file changed, 39 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index aa6bce5591..514d01c87f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13159,6 +13159,45 @@ (define-public r-seqgl
factors bound at the specific regions.")
(license license:gpl2+)))
+(define-public r-seraster
+ ;; There are no tags or releases.
+ (let ((commit "4fdc1ffe5d3feb65de9880329d221cf276b393a1")
+ (revision "1"))
+ (package
+ (name "r-seraster")
+ (version (git-version "0.99.0" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/JEFworks-Lab/SEraster")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0y33lk8q0h9nfzmf7slxxvw3l0djassp4l63nsjpm3p6z4pah5s4"))))
+ (properties `((upstream-name . "SEraster")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biocparallel
+ r-ggplot2
+ r-matrix
+ r-rearrr
+ r-sf
+ r-spatialexperiment
+ r-summarizedexperiment))
+ (home-page "https://github.com/JEFworks-Lab/SEraster")
+ (synopsis
+ "Rasterization framework for scalable spatial omics data analysis")
+ (description
+ "This package is a rasterization preprocessing framework that aggregates
+cellular information into spatial pixels to reduce resource requirements for
+spatial omics data analysis. SEraster reduces the number of points in spatial
+omics datasets for downstream analysis through a process of rasterization where
+single cells gene expression or cell-type labels are aggregated into equally
+sized pixels based on a user-defined resolution. SEraster can be incorporated
+with other packages to conduct downstream analyses for spatial omics datasets,
+such as detecting spatially variable genes.")
+ (license license:gpl3))))
+
(define-public emboss
(package
(name "emboss")
base-commit: 2d19e505f6f9f82aebc9ba8c74ba223818acd9bc
--
2.41.0
^ permalink raw reply related [relevance 14%]
* [bug#68934] [PATCH] Removed this package because there is a newer version in carn.scm
@ 2024-02-05 10:56 20% nafkhamdc
0 siblings, 0 replies; 2+ results
From: nafkhamdc @ 2024-02-05 10:56 UTC (permalink / raw)
To: 68934; +Cc: nafkhamdc
Change-Id: I3effe7c3118a3ae447243239464cc1fe7f10e637
---
gnu/packages/bioinformatics.scm | 33 ---------------------------------
1 file changed, 33 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4db6987763..56709c0332 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11134,39 +11134,6 @@ (define-public r-projectils
states in the the context of known, reference states.")
(license license:gpl3))))
-(define-public r-presto
- (let ((commit "052085db9c88aa70a28d11cc58ebc807999bf0ad")
- (revision "0"))
- (package
- (name "r-presto")
- (version (git-version "1.0.0" revision commit))
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/immunogenomics/presto")
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32 "1c3fmag4r4p2lvbvxlxyck9dvfw1prbwcl9665mmlx4a35750hk8"))))
- (properties `((upstream . "presto")))
- (build-system r-build-system)
- (propagated-inputs
- (list r-data-table
- r-deseq2
- r-dplyr
- r-matrix
- r-rcpp
- r-rcpparmadillo
- r-reshape2
- r-rlang
- r-tidyr))
- (home-page "https://github.com/immunogenomics/presto")
- (synopsis "Fast Functions for Differential Expression using Wilcox and AUC")
- (description "This package performs a fast Wilcoxon rank sum test and
-auROC analysis.")
- (license license:gpl3))))
-
(define-public r-sccustomize
(let ((commit "397374590dae2ccc0c560897dcd1ce4382c18798")
(revision "1"))
base-commit: 5a806face508cdfcd91e1eb1afb3ec38c002ec92
prerequisite-patch-id: 3a59afadab83198b19921e19197e26925523b4a3
--
2.34.1
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2024-02-05 10:56 20% [bug#68934] [PATCH] Removed this package because there is a newer version in carn.scm nafkhamdc
2024-04-23 13:29 [bug#70536] [Patch] gnu: Add r-seraster and r-rearrr MadalinIonel.Patrascu
2024-04-23 14:23 14% ` [bug#70536] [PATCH 2/2] v2 gnu: Add r-seraster Mădălin Ionel Patrașcu
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