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authorMarius Bakke <marius@gnu.org>2021-08-12 00:30:27 +0200
committerMarius Bakke <marius@gnu.org>2021-08-12 00:30:27 +0200
commitc4133c43c7cfe2476ebfae87f9e4d10d96de9bc7 (patch)
tree47bd773d2f434384b54e56916c1a287dd8e51511 /gnu/packages/bioinformatics.scm
parentffa01e68859bb7a6daa9fcffdc8d77ca35db4bc0 (diff)
parent4eb0a5146ae5a195a29c79f586fcc1e58f7fa69b (diff)
Merge branch 'master' into core-updates-frozen
Conflicts: gnu/packages/algebra.scm gnu/packages/games.scm gnu/packages/golang.scm gnu/packages/kerberos.scm gnu/packages/mail.scm gnu/packages/python.scm gnu/packages/ruby.scm gnu/packages/scheme.scm gnu/packages/tex.scm gnu/packages/tls.scm gnu/packages/version-control.scm
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm80
1 files changed, 76 insertions, 4 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 0b87d37bcf..cbc018a360 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10380,7 +10380,7 @@ once. This package provides tools to perform Drop-seq analyses.")
(define-public pigx-rnaseq
(package
(name "pigx-rnaseq")
- (version "0.0.17")
+ (version "0.0.18")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_rnaseq/"
@@ -10388,7 +10388,7 @@ once. This package provides tools to perform Drop-seq analyses.")
"/pigx_rnaseq-" version ".tar.gz"))
(sha256
(base32
- "0k9zj50bij3sjwq08v8l8waddcx8k66m3vdq8mx5vc23p19qz42s"))))
+ "1622l6grmsk0wm859rvllngx29q3v16jjvzcdq2bmrlamccrj82y"))))
(build-system gnu-build-system)
(arguments
`(#:parallel-tests? #f ; not supported
@@ -10671,7 +10671,7 @@ based methods.")
(define-public pigx-sars-cov2-ww
(package
(name "pigx-sars-cov2-ww")
- (version "0.0.2")
+ (version "0.0.3")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/BIMSBbioinfo/pigx_sarscov2_ww/"
@@ -10679,7 +10679,7 @@ based methods.")
"/pigx_sars-cov2-ww-" version ".tar.gz"))
(sha256
(base32
- "0yrbza7lbzijjc8ifk06b646n959a4k7id94x3ndz795892f64l0"))))
+ "1hhdbwsnl0d37lrmisw5hr630xr8s41qvxflm05anh11rj8n22yw"))))
(build-system gnu-build-system)
(inputs
`(("bash-minimal" ,bash-minimal)
@@ -14735,3 +14735,75 @@ ploidy and allele-specific copy number profiles.")
copy number estimation, as described by
@url{doi:10.1016/j.cell.2012.04.023,Nik-Zainal et al.}")
(license license:gpl3)))
+
+(define-public r-spectre
+ (let ((commit "f6648ab3eb9499300d86502b5d60ec370ae9b61a")
+ (revision "1"))
+ (package
+ (name "r-spectre")
+ (version (git-version "0.5.5" revision commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ImmuneDynamics/Spectre")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0g38grrhbqqa4bmcilvdyawbkcnax6k4vffx2giywp18mbirmj0x"))))
+ (properties `((upstream-name . "Spectre")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocmanager" ,r-biocmanager)
+ ("r-caret" ,r-caret)
+ ("r-class" ,r-class)
+ ("r-colorramps" ,r-colorramps)
+ ("r-data-table" ,r-data-table)
+ ("r-devtools" ,r-devtools)
+ ("r-dplyr" ,r-dplyr)
+ ("r-exactextractr" ,r-exactextractr)
+ ("r-factoextra" ,r-factoextra)
+ ("r-flowcore" ,r-flowcore)
+ ("r-flowsom" ,r-flowsom)
+ ("r-flowviz" ,r-flowviz)
+ ("r-fnn" ,r-fnn)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggpointdensity" ,r-ggpointdensity)
+ ("r-ggpubr" ,r-ggpubr)
+ ("r-ggraph" ,r-ggraph)
+ ("r-ggthemes" ,r-ggthemes)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gtools" ,r-gtools)
+ ("r-hdf5array" ,r-hdf5array)
+ ("r-irlba" ,r-irlba)
+ ("r-pheatmap" ,r-pheatmap)
+ ("r-plyr" ,r-plyr)
+ ("r-qs" ,r-qs)
+ ("r-raster" ,r-raster)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rgeos" ,r-rgeos)
+ ("r-rhdf5" ,r-rhdf5)
+ ("r-rstudioapi" ,r-rstudioapi)
+ ("r-rsvd" ,r-rsvd)
+ ("r-rtsne" ,r-rtsne)
+ ("r-s2" ,r-s2)
+ ("r-scales" ,r-scales)
+ ("r-sf" ,r-sf)
+ ("r-sp" ,r-sp)
+ ("r-stars" ,r-stars)
+ ("r-stringr" ,r-stringr)
+ ("r-tidygraph" ,r-tidygraph)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tidyr" ,r-tidyr)
+ ("r-tiff" ,r-tiff)
+ ("r-umap" ,r-umap)))
+ (home-page "https://github.com/ImmuneDynamics/Spectre")
+ (synopsis "High-dimensional cytometry and imaging analysis")
+ (description
+ "This package provides a computational toolkit in R for the
+integration, exploration, and analysis of high-dimensional single-cell
+cytometry and imaging data.")
+ (license license:expat))))