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