diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 112 |
1 files changed, 112 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3572f3d551..a414a58382 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -876,6 +876,38 @@ attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.") (license license:gpl3)))) +(define-public r-ewastools + (let ((commit "f7646cacd73266708479b3fea5d625054d179f95") + (revision "1")) + (package + (name "r-ewastools") + (version (git-version "1.7.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/hhhh5/ewastools/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0irarlnxfnasa755adxsn67rxsy01zwhjhw18g4cag08cqiyyw41")))) + (properties `((upstream-name . "ewastools"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-igraph + r-illuminaio + r-mblm + r-quadprog)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/hhhh5/ewastools/") + (synopsis + "Quality control toolset for the Illumina Infinium DNA methylation") + (description + "This package provides a collection of useful functions for working +with DNA methylation micro-array data.") + (license license:unlicense)))) + (define-public r-numbat (let ((commit "4ab7752e7d267a3f443756675728521a9b0a7295") (revision "1")) @@ -9891,6 +9923,51 @@ tasks.") Pore-C concatemers.") (license license:gpl3)))) +(define-public r-dnamcrosshyb + ;; There aren't any releases. + (let ((commit "fe8acb33667e81f00dcb84e0fa75c87ab2db5d8f") + (revision "1")) + (package + (name "r-dnamcrosshyb") + (version (git-version "0.0.0.9000" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pjhop/DNAmCrosshyb") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "12j1xsiqpvny5rp23z1az0k4cj5ajbcwkg65z00s16vywi2rx6nb")))) + (properties `((upstream-name . "DNAmCrosshyb"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-biocparallel + r-biostrings + r-bsgenome-hsapiens-ucsc-hg19-masked + r-bsgenome-hsapiens-ucsc-hg38-masked + r-dplyr + r-genomicranges + r-ggplot2 + r-iranges + r-magrittr + r-minfi + r-purrr + r-s4vectors + r-shiny + r-stringi + r-stringr + r-tibble + r-tidyr + r-watermelon)) + (home-page "https://github.com/pjhop/DNAmCrosshyb") + (synopsis "DNAmCrosshyb") + (description + "This package provides helper functions to detect cross-hybridization +on Illumina DNAm arrays.") + (license license:gpl3)))) + (define-public r-doubletcollection (let ((commit "c0d62f1853942ee6a087eaf7b000d9e4261e2dfd") (revision "1")) @@ -15580,6 +15657,41 @@ analysing cytometry data in R.") spatial single-cell expression data.") (license license:expat)))) +;; Variant of r-illuminahumanmethylationepicmanifest in the +;; (gnu packages bioconductor) module. +(define-public r-illuminahumanmethylationepicmanifest-latest + (let ((commit "a9ffbad36f5e496ece6c4c37b80e2f4f7e02d0c3") + (revision "1")) + (package + (name "r-illuminahumanmethylationepicmanifest") + (version (git-version "1.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0v8f0hl0v8gwi61vgqw56rn5j09h95hj54rb8pzbn0znm162n4fc")))) + (properties `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) + (build-system r-build-system) + (home-page + "https://github.com/achilleasNP/IlluminaHumanMethylationEPICmanifest") + (synopsis "Illumina Human Methylation Manifest 1.0 B5 for R and minfi") + (description + "This is a drop-in replacement for the +@code{IlluminaHumanMethylationEPIC} package. It utilizes a Manifest based on +1.0B5 annotation. As of version 0.3.0, the +@code{IlluminaHumanMethylationEPIC} package still employs the 1.0B2 annotation +manifest. A corresponding annotation package, +@code{IlluminaHumanMethylationEPICanno.ilm10b5.hg38}, is available to ensure +proper annotation. The decision to maintain the same name is due to +complications in downstream processing caused by array name lookup in certain +preprocessing options.") + (license license:artistic2.0)))) + (define-public r-illuminahumanmethylationepicanno-ilm10b5-hg38 (let ((commit "3db06910e27f626e0cc8b335ff45cf9a4050a36a") (revision "1")) |