diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 135 |
1 files changed, 133 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f157523a76..cb12eba7c5 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -3521,8 +3521,6 @@ annotations of the genome.") ;; remainder of the code is licensed under the MIT license. (license (list license:bsd-3 license:expat)))) -(define-deprecated deeptools python-deeptools) - (define-public cutadapt (package (name "cutadapt") @@ -13991,6 +13989,85 @@ cells with similar identification cards in the different cytometric profiles is then merged.") (license license:gpl2)))) +(define-public r-cytoexplorer + (let ((commit "0efb1cc19fc701ae03905cf1b8484c1dfeb387df") + (revision "1")) + (package + (name "r-cytoexplorer") + (version (git-version "1.1.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/DillonHammill/CytoExploreR") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1y7dadsy15i47rjmdq6ns80jzm6p0zmixll37q68ba2c7xn5pq3v")) + (snippet + '(delete-file + "docs/articles/CytoExploreR_files/vis-4.20.1/vis.min.js")))) + (properties `((upstream-name . "CytoExploreR"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'process-javascript + (lambda* (#:key inputs #:allow-other-keys) + (with-directory-excursion "docs/articles/CytoExploreR_files/" + (let ((source (search-input-file inputs "/dist/vis.js")) + (target "vis-4.20.1/vis.min.js")) + (invoke "esbuild" source "--minify" + (string-append "--outfile=" target))))))))) + (propagated-inputs + (list r-biocgenerics + r-bslib + r-data-table + r-dplyr + r-embedsom + r-flowai + r-flowcore + r-flowworkspace + r-gtools + r-magrittr + r-mass + r-opencyto + r-purrr + r-rhandsontable + r-robustbase + r-rsvd + r-rtsne + r-shiny + r-superheat + r-tibble + r-tidyr + r-umap + r-visnetwork)) + (native-inputs + `(("esbuild" ,esbuild) + ("r-knitr" ,r-knitr) + ("js-vis" + ,(let ((version "4.20.1")) + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/almende/vis") + (commit (string-append "v" version)))) + (file-name (git-file-name "js-vis" version)) + (sha256 + (base32 + "09ldcqzzki5c0jlwas5992qjffqxnx6j5sl703qccfw7rg1hn469"))))))) + (home-page "https://github.com/DillonHammill/CytoExploreR") + (synopsis "Interactive analysis of cytometry data") + (description + "This package has been developed under ROpenSci gudelines to integrate +conventional and cutting edge cytometry analysis tools under a unified +framework. It aims to represent an intuitive and interactive approach to +analysing cytometry data in R.") + (license license:gpl2)))) + (define-public r-giotto (let ((commit "3c8067cedbf6e3112edcac2ae796de05fd9d6fe4") (revision "1")) @@ -14049,6 +14126,60 @@ is then merged.") spatial single-cell expression data.") (license license:expat)))) +(define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38 + (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a") + (revision "1")) + (package + (name "r-illuminahumanmethylationepicanno-ilm10b5-hg38") + (version (git-version "0.0.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0y8fhiwmkldi57f8nq64njfgljw68cm6pb1vh44hjwcc12k48sqr")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICanno.ilm10b5.hg38"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi)) + (home-page + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICanno.ilm10b5.hg38") + (synopsis "Illumina Human Methylation EPIC Annotation version 1.0B5") + (description + "This package provides a companion annotation file to the +@code{IlluminaHumanMethylationEPICmanifest} package based on the same +annotation 1.0B5.") + (license license:artistic2.0)))) + +(define-public r-maxprobes + (let ((commit "c2120dba972e12115280ef274ff80550cee5b264") + (revision "1")) + (package + (name "r-maxprobes") + (version (git-version "0.0.2" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/markgene/maxprobes") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1kij9bds2l9mwm519bzyd2608563qjlmbrayhva1s0vgml5iq9wh")))) + (properties `((upstream-name . "maxprobes"))) + (build-system r-build-system) + (propagated-inputs (list r-minfi r-minfidata)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/markgene/maxprobes") + (synopsis "Methylation array cross-reactive probes") + (description + "The Maxprobes package collects cross-reactive probes of Illumina +methylation array 450K and EPIC/850K.") + (license license:gpl2+)))) + (define-public gffread ;; We cannot use the tagged release because it is not in sync with gclib. ;; See https://github.com/gpertea/gffread/issues/26 |