diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 77 |
1 files changed, 75 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 7972b6e55c..d3ff0b1127 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -37,10 +37,12 @@ #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) + #:use-module (gnu packages algebra) #:use-module (gnu packages autotools) #:use-module (gnu packages base) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) + #:use-module (gnu packages chemistry) #:use-module (gnu packages cran) #:use-module (gnu packages compression) #:use-module (gnu packages curl) @@ -66,6 +68,36 @@ ;;; Annotations +(define-public r-mafh5-gnomad-v3-1-2-grch38 + (package + (name "r-mafh5-gnomad-v3-1-2-grch38") + (version "3.15.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MafH5.gnomAD.v3.1.2.GRCh38" version + 'annotation)) + (sha256 + (base32 "18hzw7f41ii16qpm3ch516b773900l1m1id5z6a763m01fg0mhiq")))) + (properties `((upstream-name . "MafH5.gnomAD.v3.1.2.GRCh38"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome + r-genomeinfodb + r-genomicranges + r-genomicscores + r-hdf5array + r-iranges + r-rhdf5 + r-s4vectors)) + (home-page "https://bioconductor.org/packages/MafH5.gnomAD.v3.1.2.GRCh38") + (synopsis + "Minor allele frequency data from gnomAD version 3.1.2 for GRCh38") + (description + "This package is designed to store minor allele frequency data. +It retrieves this data from the Genome Aggregation Database +(@code{gnomAD} version 3.1.2) for the human genome version GRCh38.") + (license license:artistic2.0))) + (define-public r-org-eck12-eg-db (package (name "r-org-eck12-eg-db") @@ -18852,6 +18884,47 @@ coordinate plots, volcano plots, and litre plots. It includes examples for visualizing RNA-sequencing datasets and differentially expressed genes.") (license license:gpl3))) +(define-public r-chemmineob + (package + (name "r-chemmineob") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ChemmineOB" version)) + (sha256 + (base32 "0l44d6l078k1w5nf7i4sarah1zn30zqjmcj9qpy4hhg97dfy45ci")))) + (properties `((upstream-name . "ChemmineOB"))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-makefile + (lambda _ + (substitute* "src/Makevars.in" + (("/usr/include/openbabel3") + (string-append #$(this-package-input "openbabel") + "/include/openbabel3")) + (("/usr/include/eigen3") + (string-append #$(this-package-input "eigen") + "/include/eigen3")))))))) + (inputs (list eigen openbabel)) + (propagated-inputs (list r-bh r-biocgenerics r-rcpp r-zlibbioc)) + (native-inputs (list pkg-config r-knitr)) + (home-page "https://github.com/girke-lab/ChemmineOB") + (synopsis "R interface to a subset of OpenBabel functionalities") + (description + "@code{ChemmineOB} provides an R interface to a subset of cheminformatics +functionalities implemented by the @code{OpelBabel} C++ project. +@code{OpenBabel} is an open source cheminformatics toolbox that includes +utilities for structure format interconversions, descriptor calculations, +compound similarity searching and more. @code{ChemineOB} aims to make a subset +of these utilities available from within R. For non-developers, +@code{ChemineOB} is primarily intended to be used from @code{ChemmineR} as an +add-on package rather than used directly.") + (license license:asl2.0))) + (define-public r-chemminer (package (name "r-chemminer") @@ -21397,14 +21470,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "3.0.0") + (version "3.0.1") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "100nafmyddz0c1h01fbqw5q6pji7zhg2196rkyak88za6s5ms0s4")))) + "03g02450l3mckjzwd0w717dbmxhrngkwlfhm5c9q5zv4g10df7nj")))) (build-system r-build-system) (inputs (list gsl)) |