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| -rw-r--r-- | gnu/packages/bioconductor.scm | 47 |
1 files changed, 47 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index d2a296ff66..fd9ff0c678 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -3417,6 +3417,53 @@ users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package: +;; r-biomart +(define-public r-biomartr + (package + (name "r-biomartr") + (version "1.0.2") + (source (origin + (method url-fetch) + (uri (cran-uri "biomartr" version)) + (sha256 + (base32 + "0hr7wks88lbfcqzjzm4x265dk4lpmc3i2ndp7xcrx8ssj76wrmkz")))) + (properties `((upstream-name . "biomartr"))) + (build-system r-build-system) + (propagated-inputs + (list r-biomart + r-biostrings + r-curl + r-data-table + r-downloader + r-dplyr + r-fs + r-httr + r-jsonlite + r-philentropy + r-purrr + r-r-utils + r-rcurl + r-readr + r-stringr + r-tibble + r-withr + r-xml)) + (native-inputs (list r-knitr)) + (home-page "https://docs.ropensci.org/biomartr/") + (synopsis "Genomic data retrieval") + (description + "Perform large scale genomic data retrieval and functional annotation +retrieval. This package aims to provide users with a standardized way to +automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome +retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases. +Furthermore, an interface to the BioMart database allows users to retrieve +functional annotation for genomic loci. In addition, users can download +entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with +only one command.") + (license license:gpl2))) + (define-public r-biocparallel (package (name "r-biocparallel") |