gnu: r-gkmsvm: Move to (gnu packages bioconductor).
* gnu/packages/bioinformatics.scm (r-gkmsvm): Move from here... * gnu/packages/bioconductor.scm (r-gkmsvm): ...to here.master
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@ -2521,3 +2521,37 @@ summaries of the read-types produced, it provides a number of plots for
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visualising metrics relative to experiment run time or spatially over the
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visualising metrics relative to experiment run time or spatially over the
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surface of a flowcell.")
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surface of a flowcell.")
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(license license:expat)))
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(license license:expat)))
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;; This is a CRAN package, but it depends on packages from Bioconductor.
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(define-public r-gkmsvm
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(package
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(name "r-gkmsvm")
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(version "0.79.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "gkmSVM" version))
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(sha256
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(base32
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"04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
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(properties `((upstream-name . "gkmSVM")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-kernlab" ,r-kernlab)
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("r-rcpp" ,r-rcpp)
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("r-rocr" ,r-rocr)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-seqinr" ,r-seqinr)))
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(home-page "https://cran.r-project.org/web/packages/gkmSVM")
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(synopsis "Gapped-kmer support vector machine")
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(description
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"This R package provides tools for training gapped-kmer SVM classifiers
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for DNA and protein sequences. This package supports several sequence
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kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
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(license license:gpl2+)))
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@ -8533,39 +8533,6 @@ bound and non bound genomic regions to accurately identify transcription
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factors bound at the specific regions.")
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factors bound at the specific regions.")
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(license license:gpl2+)))
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(license license:gpl2+)))
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(define-public r-gkmsvm
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(package
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(name "r-gkmsvm")
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(version "0.79.0")
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(source
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(origin
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(method url-fetch)
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(uri (cran-uri "gkmSVM" version))
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(sha256
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(base32
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"04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3"))))
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(properties `((upstream-name . "gkmSVM")))
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(build-system r-build-system)
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(propagated-inputs
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`(("r-biocgenerics" ,r-biocgenerics)
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("r-biostrings" ,r-biostrings)
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("r-genomeinfodb" ,r-genomeinfodb)
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("r-genomicranges" ,r-genomicranges)
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("r-iranges" ,r-iranges)
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("r-kernlab" ,r-kernlab)
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("r-rcpp" ,r-rcpp)
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("r-rocr" ,r-rocr)
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("r-rtracklayer" ,r-rtracklayer)
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("r-s4vectors" ,r-s4vectors)
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("r-seqinr" ,r-seqinr)))
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(home-page "https://cran.r-project.org/web/packages/gkmSVM")
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(synopsis "Gapped-kmer support vector machine")
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(description
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"This R package provides tools for training gapped-kmer SVM classifiers
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for DNA and protein sequences. This package supports several sequence
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kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.")
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(license license:gpl2+)))
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(define-public r-tximport
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(define-public r-tximport
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(package
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(package
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(name "r-tximport")
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(name "r-tximport")
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