+
+(define-public r-riboprofiling
+ (package
+ (name "r-riboprofiling")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RiboProfiling" version))
+ (sha256
+ (base32
+ "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
+ (properties `((upstream-name . "RiboProfiling")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-biostrings" ,r-biostrings)
+ ("r-data-table" ,r-data-table)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggbio" ,r-ggbio)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-iranges" ,r-iranges)
+ ("r-plyr" ,r-plyr)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-sqldf" ,r-sqldf)))
+ (home-page "https://bioconductor.org/packages/RiboProfiling/")
+ (synopsis "Ribosome profiling data analysis")
+ (description "Starting with a BAM file, this package provides the
+necessary functions for quality assessment, read start position recalibration,
+the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
+of count data: pairs, log fold-change, codon frequency and coverage
+assessment, principal component analysis on codon coverage.")
+ (license license:gpl3)))
+
+(define-public r-riboseqr
+ (package
+ (name "r-riboseqr")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "riboSeqR" version))
+ (sha256
+ (base32
+ "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
+ (properties `((upstream-name . "riboSeqR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-abind" ,r-abind)
+ ("r-bayseq" ,r-bayseq)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-seqlogo" ,r-seqlogo)))
+ (home-page "https://bioconductor.org/packages/riboSeqR/")
+ (synopsis "Analysis of sequencing data from ribosome profiling experiments")
+ (description
+ "This package provides plotting functions, frameshift detection and
+parsing of genetic sequencing data from ribosome profiling experiments.")
+ (license license:gpl3)))
+
+(define-public r-interactionset
+ (package
+ (name "r-interactionset")
+ (version "1.10.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "InteractionSet" version))
+ (sha256
+ (base32
+ "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
+ (properties
+ `((upstream-name . "InteractionSet")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocgenerics" ,r-biocgenerics)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (home-page "https://bioconductor.org/packages/InteractionSet")
+ (synopsis "Base classes for storing genomic interaction data")
+ (description
+ "This packages provides the @code{GInteractions},
+@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
+for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
+experiments.")
+ (license license:gpl3)))
+
+(define-public r-genomicinteractions
+ (package
+ (name "r-genomicinteractions")
+ (version "1.16.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "GenomicInteractions" version))
+ (sha256
+ (base32
+ "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
+ (properties
+ `((upstream-name . "GenomicInteractions")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-gviz" ,r-gviz)
+ ("r-igraph" ,r-igraph)
+ ("r-interactionset" ,r-interactionset)
+ ("r-iranges" ,r-iranges)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-rtracklayer" ,r-rtracklayer)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-stringr" ,r-stringr)))
+ (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
+ (synopsis "R package for handling genomic interaction data")
+ (description
+ "This R package provides tools for handling genomic interaction data,
+such as ChIA-PET/Hi-C, annotating genomic features with interaction
+information and producing various plots and statistics.")
+ (license license:gpl3)))
+
+(define-public r-ctc
+ (package
+ (name "r-ctc")
+ (version "1.56.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ctc" version))
+ (sha256
+ (base32
+ "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
+ (build-system r-build-system)
+ (propagated-inputs `(("r-amap" ,r-amap)))
+ (home-page "https://bioconductor.org/packages/ctc/")
+ (synopsis "Cluster and tree conversion")
+ (description
+ "This package provides tools for exporting and importing classification
+trees and clusters to other programs.")
+ (license license:gpl2)))
+
+(define-public r-goseq
+ (package
+ (name "r-goseq")
+ (version "1.34.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "goseq" version))
+ (sha256
+ (base32
+ "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-annotationdbi" ,r-annotationdbi)
+ ("r-biasedurn" ,r-biasedurn)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-genelendatabase" ,r-genelendatabase)
+ ("r-go-db" ,r-go-db)
+ ("r-mgcv" ,r-mgcv)))
+ (home-page "https://bioconductor.org/packages/goseq/")
+ (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
+ (description
+ "This package provides tools to detect Gene Ontology and/or other user
+defined categories which are over/under represented in RNA-seq data.")
+ (license license:lgpl2.0+)))
+
+(define-public r-glimma
+ (package
+ (name "r-glimma")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Glimma" version))
+ (sha256
+ (base32
+ "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
+ (properties `((upstream-name . "Glimma")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-edger" ,r-edger)
+ ("r-jsonlite" ,r-jsonlite)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://github.com/Shians/Glimma")
+ (synopsis "Interactive HTML graphics")
+ (description
+ "This package generates interactive visualisations for analysis of
+RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
+HTML page. The interactions are built on top of the popular static
+representations of analysis results in order to provide additional
+information.")
+ (license license:lgpl3)))
+
+(define-public r-rots
+ (package
+ (name "r-rots")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ROTS" version))
+ (sha256
+ (base32
+ "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
+ (properties `((upstream-name . "ROTS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/ROTS/")
+ (synopsis "Reproducibility-Optimized Test Statistic")
+ (description
+ "This package provides tools for calculating the
+@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
+in omics data.")
+ (license license:gpl2+)))
+
+(define-public r-plgem
+ (package
+ (name "r-plgem")
+ (version "1.54.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "plgem" version))
+ (sha256
+ (base32
+ "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-mass" ,r-mass)))
+ (home-page "http://www.genopolis.it")
+ (synopsis "Detect differential expression in microarray and proteomics datasets")
+ (description
+ "The Power Law Global Error Model (PLGEM) has been shown to faithfully
+model the variance-versus-mean dependence that exists in a variety of
+genome-wide datasets, including microarray and proteomics data. The use of
+PLGEM has been shown to improve the detection of differentially expressed
+genes or proteins in these datasets.")
+ (license license:gpl2)))
+
+(define-public r-inspect
+ (package
+ (name "r-inspect")
+ (version "1.12.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "INSPEcT" version))
+ (sha256
+ (base32
+ "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
+ (properties `((upstream-name . "INSPEcT")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-biocparallel" ,r-biocparallel)
+ ("r-deseq2" ,r-deseq2)
+ ("r-desolve" ,r-desolve)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicfeatures" ,r-genomicfeatures)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-iranges" ,r-iranges)
+ ("r-plgem" ,r-plgem)
+ ("r-preprocesscore" ,r-preprocesscore)
+ ("r-proc" ,r-proc)
+ ("r-rootsolve" ,r-rootsolve)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-shiny" ,r-shiny)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-txdb-mmusculus-ucsc-mm9-knowngene"
+ ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
+ (home-page "https://bioconductor.org/packages/INSPEcT")
+ (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
+ (description
+ "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
+Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
+order to evaluate synthesis, processing and degradation rates and assess via
+modeling the rates that determines changes in mature mRNA levels.")
+ (license license:gpl2)))
+
+(define-public r-dnabarcodes
+ (package
+ (name "r-dnabarcodes")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "DNABarcodes" version))
+ (sha256
+ (base32
+ "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
+ (properties `((upstream-name . "DNABarcodes")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-bh" ,r-bh)
+ ("r-matrix" ,r-matrix)
+ ("r-rcpp" ,r-rcpp)))
+ (home-page "https://bioconductor.org/packages/DNABarcodes")
+ (synopsis "Create and analyze DNA barcodes")
+ (description
+ "This package offers tools to create DNA barcode sets capable of
+correcting insertion, deletion, and substitution errors. Existing barcodes
+can be analyzed regarding their minimal, maximal and average distances between
+barcodes. Finally, reads that start with a (possibly mutated) barcode can be
+demultiplexed, i.e. assigned to their original reference barcode.")
+ (license license:gpl2)))
+
+(define-public r-ruvseq
+ (package
+ (name "r-ruvseq")
+ (version "1.16.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "RUVSeq" version))
+ (sha256
+ (base32
+ "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
+ (properties `((upstream-name . "RUVSeq")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-edaseq" ,r-edaseq)
+ ("r-edger" ,r-edger)
+ ("r-mass" ,r-mass)))
+ (home-page "https://github.com/drisso/RUVSeq")
+ (synopsis "Remove unwanted variation from RNA-Seq data")
+ (description
+ "This package implements methods to @dfn{remove unwanted variation} (RUV)
+of Risso et al. (2014) for the normalization of RNA-Seq read counts between
+samples.")
+ (license license:artistic2.0)))
+
+(define-public r-biocneighbors
+ (package
+ (name "r-biocneighbors")
+ (version "1.0.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BiocNeighbors" version))
+ (sha256
+ (base32
+ "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
+ (properties `((upstream-name . "BiocNeighbors")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppannoy" ,r-rcppannoy)
+ ("r-s4vectors" ,r-s4vectors)))
+ (home-page "https://bioconductor.org/packages/BiocNeighbors")
+ (synopsis "Nearest Neighbor Detection for Bioconductor packages")
+ (description
+ "This package implements exact and approximate methods for nearest
+neighbor detection, in a framework that allows them to be easily switched
+within Bioconductor packages or workflows. The exact algorithm is implemented
+using pre-clustering with the k-means algorithm. Functions are also provided
+to search for all neighbors within a given distance. Parallelization is
+achieved for all methods using the BiocParallel framework.")
+ (license license:gpl3)))
+
+(define-public r-destiny
+ (package
+ (name "r-destiny")
+ (version "2.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "destiny" version))
+ (sha256
+ (base32
+ "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biobase" ,r-biobase)
+ ("r-biocgenerics" ,r-biocgenerics)
+ ("r-fnn" ,r-fnn)
+ ("r-ggthemes" ,r-ggthemes)
+ ("r-hmisc" ,r-hmisc)
+ ("r-igraph" ,r-igraph)
+ ("r-matrix" ,r-matrix)
+ ("r-proxy" ,r-proxy)
+ ("r-rcpp" ,r-rcpp)
+ ("r-rcppeigen" ,r-rcppeigen)
+ ("r-scales" ,r-scales)
+ ("r-scatterplot3d" ,r-scatterplot3d)
+ ("r-smoother" ,r-smoother)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)
+ ("r-vim" ,r-vim)))
+ (home-page "https://bioconductor.org/packages/destiny/")
+ (synopsis "Create and plot diffusion maps")
+ (description "This package provides tools to create and plot diffusion
+maps.")
+ ;; Any version of the GPL
+ (license license:gpl3+)))
+
+(define-public r-savr
+ (package
+ (name "r-savr")
+ (version "1.20.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "savR" version))
+ (sha256
+ (base32
+ "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
+ (properties `((upstream-name . "savR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-ggplot2" ,r-ggplot2)
+ ("r-gridextra" ,r-gridextra)
+ ("r-reshape2" ,r-reshape2)
+ ("r-scales" ,r-scales)
+ ("r-xml" ,r-xml)))
+ (home-page "https://github.com/bcalder/savR")
+ (synopsis "Parse and analyze Illumina SAV files")
+ (description
+ "This package provides tools to parse Illumina Sequence Analysis
+Viewer (SAV) files, access data, and generate QC plots.")
+ (license license:agpl3+)))
+
+(define-public r-chipexoqual
+ (package
+ (name "r-chipexoqual")
+ (version "1.6.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ChIPexoQual" version))
+ (sha256
+ (base32
+ "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
+ (properties `((upstream-name . "ChIPexoQual")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-biocparallel" ,r-biocparallel)
+ ("r-biovizbase" ,r-biovizbase)
+ ("r-broom" ,r-broom)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-genomeinfodb" ,r-genomeinfodb)
+ ("r-genomicalignments" ,r-genomicalignments)
+ ("r-genomicranges" ,r-genomicranges)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-hexbin" ,r-hexbin)
+ ("r-iranges" ,r-iranges)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-rmarkdown" ,r-rmarkdown)
+ ("r-rsamtools" ,r-rsamtools)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-viridis" ,r-viridis)))
+ (home-page "https://github.com/keleslab/ChIPexoQual")
+ (synopsis "Quality control pipeline for ChIP-exo/nexus data")
+ (description
+ "This package provides a quality control pipeline for ChIP-exo/nexus
+sequencing data.")
+ (license license:gpl2+)))