diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 80 |
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)))) |