downloaded from Encode.")
(license license:gpl3+)))
+(define-public r-macrophage
+ (package
+ (name "r-macrophage")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "macrophage" version
+ 'experiment))
+ (sha256
+ (base32
+ "0ml8v92w021fmzsn4yl90ap3l4l3b9c1pk8pzsrm122p82wzlyms"))))
+ (properties `((upstream-name . "macrophage")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/macrophage")
+ (synopsis "Human macrophage immune response data")
+ (description
+ "This package provides the output of running @code{Salmon} on a set of 24
+RNA-seq samples from Alasoo, et al. \"Shared genetic effects on chromatin and
+gene expression indicate a role for enhancer priming in immune response\", published
+in Nature Genetics, January 2018.")
+ (license license:gpl2+)))
+
(define-public r-msdata
(package
(name "r-msdata")
TCGAbiolinksGUI package.")
(license license:gpl3)))
+(define-public r-tximportdata
+ (package
+ (name "r-tximportdata")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "tximportData" version
+ 'experiment))
+ (sha256
+ (base32
+ "0mgbwpybg2xd6x1ijrflmjh5w63qz6ylnzszbbyp437n618m7riy"))))
+ (properties `((upstream-name . "tximportData")))
+ (build-system r-build-system)
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/tximportData")
+ (synopsis "Data for the tximport package")
+ (description
+ "This package provides the output of running various transcript abundance
+quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The
+quantifiers were @code{Cufflinks}, @code{RSEM}, @code{kallisto}, @code{Salmon}
+and @code{Sailfish}. Alevin example output is also included.")
+ (license license:gpl2+)))
+
+
\f
;;; Packages
tumor samples from healthy controls.")
(license license:artistic2.0)))
+(define-public r-assessorf
+ (package
+ (name "r-assessorf")
+ (version "1.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AssessORF" version))
+ (sha256
+ (base32
+ "1l87bpny9k3jbzbzmb9h2ijvblrj471gqv26fyzbvb3vr6y406z7"))))
+ (properties `((upstream-name . "AssessORF")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biostrings
+ r-decipher
+ r-genomicranges
+ r-iranges))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/AssessORF")
+ (synopsis "Assess gene predictions using proteomics and evolutionary conservation")
+ (description
+ "In order to assess the quality of a set of predicted genes for a genome,
+evidence must first be mapped to that genome. Next, each gene must be
+categorized based on how strong the evidence is for or against that gene. The
+AssessORF package provides the functions and class structures necessary for
+accomplishing those tasks, using proteomics hits and evolutionarily conserved
+start codons as the forms of evidence.")
+ (license license:gpl3)))
+
+(define-public r-asset
+ (package
+ (name "r-asset")
+ (version "2.14.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "ASSET" version))
+ (sha256
+ (base32
+ "029acl5k9d4hnvy3jia9cr4rk6w31zn8b5s79i6lazq1cp236hbg"))))
+ (properties `((upstream-name . "ASSET")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-mass r-msm r-rmeta))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/ASSET")
+ (synopsis
+ "Subset-based association analysis of heterogeneous traits and subtypes")
+ (description
+ "This package is an R program for the subset-based analysis of
+heterogeneous traits and disease subtypes. ASSET allows the user to search
+through all possible subsets of z-scores to identify the subset of traits
+giving the best meta-analyzed z-score. Further, it returns a p-value
+adjusting for the multiple-testing involved in the search. It also allows for
+searching for the best combination of disease subtypes associated with each
+variant.")
+ (license license:gpl2)))
+
+(define-public r-atena
+ (package
+ (name "r-atena")
+ (version "1.2.2")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "atena" version))
+ (sha256
+ (base32
+ "0b89wb7cc44c8jd6868dn8pwgid768bprkncsi87qkdz0abbhzhp"))))
+ (properties `((upstream-name . "atena")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationhub
+ r-biocgenerics
+ r-biocparallel
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-iranges
+ r-matrix
+ r-rsamtools
+ r-s4vectors
+ r-scales
+ r-sparsematrixstats
+ r-squarem
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/functionalgenomics/atena")
+ (synopsis "Analysis of transposable elements")
+ (description
+ "The atena package quantifies expression of @dfn{TEs} (transposable
+elements) from RNA-seq data through different methods, including ERVmap,
+TEtranscripts and Telescope. A common interface is provided to use each of
+these methods, which consists of building a parameter object, calling the
+quantification function with this object and getting a
+@code{SummarizedExperiment} object as an output container of the quantified
+expression profiles. The implementation allows quantifing TEs and gene
+transcripts in an integrated manner.")
+ (license license:artistic2.0)))
+
+(define-public r-atsnp
+ (package
+ (name "r-atsnp")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "atSNP" version))
+ (sha256
+ (base32
+ "0dmv34xqwr3l2rznapxmyrkyf1w78qzxdv88s5nn8s1m8qdkgwkz"))))
+ (properties `((upstream-name . "atSNP")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocfilecache
+ r-biocparallel
+ r-bsgenome
+ r-data-table
+ r-ggplot2
+ r-lifecycle
+ r-motifstack
+ r-rappdirs
+ r-rcpp
+ r-testthat))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/sunyoungshin/atSNP")
+ (synopsis
+ "Affinity test for identifying regulatory single nucleotide polymorphisms")
+ (description
+ "The atSNP package performs affinity tests of motif matches with the
+@dfn{SNP} (single nucleotide polymorphism) or the reference genomes and
+SNP-led changes in motif matches.")
+ (license license:gpl2)))
+
+(define-public r-attract
+ (package
+ (name "r-attract")
+ (version "1.48.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "attract" version))
+ (sha256
+ (base32
+ "0f1fsv278kpnxvqg9qa5rw2k3zr8zws0ab73ldl60h6pv9cy8x82"))))
+ (properties `((upstream-name . "attract")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-biobase
+ r-cluster
+ r-gostats
+ r-keggrest
+ r-limma
+ r-org-hs-eg-db
+ r-reactome-db))
+ (home-page "https://bioconductor.org/packages/attract")
+ (synopsis "Finding drivers of Kauffman's attractor landscape")
+ (description
+ "This package contains the functions to find the gene expression modules
+that represent the drivers of Kauffman's attractor landscape. The modules are
+the core attractor pathways that discriminate between different cell types of
+groups of interest. Each pathway has a set of synexpression groups, which show
+transcriptionally-coordinated changes in gene expression.")
+ (license license:lgpl2.0+)))
+
+(define-public r-awfisher
+ (package
+ (name "r-awfisher")
+ (version "1.10.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "AWFisher" version))
+ (sha256
+ (base32
+ "050k7w0azsl7rqx2pxgccihzc2q8pmh6fyy4gib2d42sdyijr2n1"))))
+ (properties `((upstream-name . "AWFisher")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-edger
+ r-limma))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/AWFisher")
+ (synopsis "Fast computing for adaptively weighted fisher's method")
+ (description
+ "This package is an implementation of the Adaptively Weighted Fisher's
+method, including fast p-value computing, variability index, and
+meta-pattern.")
+ (license license:gpl3)))
+
+(define-public r-awst
+ (package
+ (name "r-awst")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "awst" version))
+ (sha256
+ (base32
+ "0iw3zycmj95rmdx7f2w0j4yxkzd90y87lrzgdn9cyvvzi5avflav"))))
+ (properties `((upstream-name . "awst")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/drisso/awst")
+ (synopsis "Asymmetric within-sample transformation")
+ (description
+ "This package @dfn{awst} (Asymmetric Within-Sample Transformation) that
+regularizes RNA-seq read counts and reduces the effect of noise on the
+classification of samples. AWST comprises two main steps: standardization and
+smoothing. These steps transform gene expression data to reduce the noise of
+the lowly expressed features, which suffer from background effects and low
+signal-to-noise ratio, and the influence of the highly expressed features,
+which may be the result of amplification bias and other experimental
+artifacts.")
+ (license license:expat)))
+
+(define-public r-baalchip
+ (package
+ (name "r-baalchip")
+ (version "1.22.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BaalChIP" version))
+ (sha256
+ (base32
+ "02qwk9n2fyg5f9xxjiiha9mi6p9ii3zi5x7w84sh5d5g58s27g6q"))))
+ (properties `((upstream-name . "BaalChIP")))
+ (build-system r-build-system)
+ (inputs (list perl)) ; extra/get.overlaps.v2_chrXY.perl
+ (propagated-inputs
+ (list r-coda
+ r-doby
+ r-doparallel
+ r-foreach
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicranges
+ r-ggplot2
+ r-iranges
+ r-reshape2
+ r-rsamtools
+ r-scales))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/BaalChIP")
+ (synopsis
+ "Analysis of allele-specific transcription factor binding in cancer genomes")
+ (description
+ "This package offers functions to process multiple @code{ChIP-seq BAM}
+files and detect allele-specific events. It computes allele counts at
+individual variants (SNPs/SNVs), implements extensive @dfn{QC} (quality
+control) steps to remove problematic variants, and utilizes a Bayesian
+framework to identify statistically significant allele-specific events.
+BaalChIP is able to account for copy number differences between the two
+alleles, a known phenotypical feature of cancer samples.")
+ (license license:artistic2.0)))
+
+(define-public r-basespacer
+ (package
+ (name "r-basespacer")
+ (version "1.40.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BaseSpaceR" version))
+ (sha256
+ (base32
+ "0jyw4pnybsd6ywpaamk5ywkrcib2z48farsnszmwq97zlbmra7fj"))))
+ (properties `((upstream-name . "BaseSpaceR")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-rcurl r-rjsonio))
+ (home-page "https://bioconductor.org/packages/BaseSpaceR")
+ (synopsis "R SDK for BaseSpace RESTful API")
+ (description
+ "This package provides an R interface to Illumina's BaseSpace cloud
+computing environment, enabling the fast development of data analysis and
+visualization tools. Besides providing an easy to use set of tools for
+manipulating the data from BaseSpace, it also facilitates the access to R's
+rich environment of statistical and data analysis tools.")
+ (license license:asl2.0)))
+
+(define-public r-bac
+ (package
+ (name "r-bac")
+ (version "1.56.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BAC" version))
+ (sha256
+ (base32
+ "0dkw7438d2sf6nb577dnzija54qs0nhlr47lb73li60fhlnvqmh2"))))
+ (properties `((upstream-name . "BAC")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/BAC")
+ (synopsis "Bayesian analysis of Chip-chip experiment")
+ (description
+ "This package uses a Bayesian hierarchical model to detect enriched
+regions from ChIP-chip experiments. The common goal in analyzing this
+ChIP-chip data is to detect DNA-protein interactions from ChIP-chip
+experiments. The BAC package has mainly been tested with Affymetrix tiling
+array data. However, we expect it to work with other platforms (e.g. Agilent,
+Nimblegen, cDNA, etc.). Note that BAC does not deal with normalization, so
+you will have to normalize your data beforehand.")
+ (license license:artistic2.0)))
+
+(define-public r-bader
+ (package
+ (name "r-bader")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BADER" version))
+ (sha256
+ (base32
+ "0i5x1r2ns1hxhqk5jyfqird81hck1hllvvgx5bn0rb5vl99g8spm"))))
+ (properties `((upstream-name . "BADER")))
+ (build-system r-build-system)
+ (home-page "https://bioconductor.org/packages/BADER")
+ (synopsis
+ "Bayesian analysis of differential expression in RNA sequencing data")
+ (description
+ "The BADER package is intended for the analysis of RNA sequencing data.
+The algorithm fits a Bayesian hierarchical model for RNA sequencing count
+data. BADER returns the posterior probability of differential expression for
+each gene between two groups A and B. The joint posterior distribution of the
+variables in the model can be returned in the form of posterior samples, which
+can be used for further down-stream analyses such as gene set enrichment.")
+ (license license:gpl2)))
+
+(define-public r-badregionfinder
+ (package
+ (name "r-badregionfinder")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BadRegionFinder" version))
+ (sha256
+ (base32
+ "1a1pqmh5ak9s3k1lxw6flanchk24zyznwm34ixi2b78wdc3hqgm9"))))
+ (properties `((upstream-name . "BadRegionFinder")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biomart
+ r-genomicranges
+ r-rsamtools
+ r-s4vectors
+ r-variantannotation))
+ (home-page "https://bioconductor.org/packages/BadRegionFinder")
+ (synopsis "Identifying regions with bad coverage in sequence alignment data")
+ (description
+ "BadRegionFinder is a package for identifying regions with a bad,
+acceptable and good coverage in sequence alignment data available as bam
+files. The whole genome may be considered as well as a set of target regions.
+Various visual and textual types of output are available.")
+ (license license:lgpl3)))
+
+(define-public r-bambu
+ (package
+ (name "r-bambu")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bambu" version))
+ (sha256
+ (base32
+ "0dc2hpnykr575jbrq9whmdabknl70s2hcs6gkmkl4kpv7xfqdq6w"))))
+ (properties `((upstream-name . "bambu")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biocparallel
+ r-bsgenome
+ r-data-table
+ r-dplyr
+ r-genomeinfodb
+ r-genomicalignments
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rcpp
+ r-rcpparmadillo
+ r-rsamtools
+ r-s4vectors
+ r-summarizedexperiment
+ r-tidyr
+ r-xgboost))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/GoekeLab/bambu")
+ (synopsis
+ "Isoform reconstruction and quantification for long read RNA-Seq data")
+ (description
+ "This R package is for multi-sample transcript discovery and
+quantification using long read RNA-Seq data. You can use bambu after read
+alignment to obtain expression estimates for known and novel transcripts and
+genes. The output from bambu can directly be used for visualisation and
+downstream analysis, such as differential gene expression or transcript
+usage.")
+ (license license:gpl3)))
+
+(define-public r-bandits
+ (package
+ (name "r-bandits")
+ (version "1.12.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "BANDITS" version))
+ (sha256
+ (base32
+ "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9"))))
+ (properties `((upstream-name . "BANDITS")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocparallel
+ r-data-table
+ r-doparallel
+ r-dorng
+ r-drimseq
+ r-foreach
+ r-ggplot2
+ r-mass
+ r-r-utils
+ r-rcpp
+ r-rcpparmadillo))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/SimoneTiberi/BANDITS")
+ (synopsis "Bayesian analysis of differential splicing")
+ (description
+ "BANDITS is a Bayesian hierarchical model for detecting differential
+splicing of genes and transcripts, via @dfn{DTU} (differential transcript
+usage), between two or more conditions. The method uses a Bayesian
+hierarchical framework, which allows for sample specific proportions in a
+Dirichlet-Multinomial model, and samples the allocation of fragments to the
+transcripts. Parameters are inferred via @dfn{MCMC} (Markov chain Monte
+Carlo) techniques and a DTU test is performed via a multivariate Wald test on
+the posterior densities for the average relative abundance of transcripts.")
+ (license license:gpl3+)))
+
+(define-public r-banocc
+ (package
+ (name "r-banocc")
+ (version "1.20.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "banocc" version))
+ (sha256
+ (base32
+ "10vaggq1w5jkxd8r2k1mhymzvb7x3h8afwn2pvmcpj022ka7xhbx"))))
+ (properties `((upstream-name . "banocc")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-coda
+ r-mvtnorm
+ r-rstan
+ r-stringr))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/banocc")
+ (synopsis "Bayesian analysis of compositional covariance")
+ (description
+ "BAnOCC is a package designed for compositional data, where each sample
+sums to one. It infers the approximate covariance of the unconstrained data
+using a Bayesian model coded with @code{rstan}. It provides as output the
+@code{stanfit} object as well as posterior median and credible interval
+estimates for each correlation element.")
+ (license license:expat)))
+
+(define-public r-barcodetrackr
+ (package
+ (name "r-barcodetrackr")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "barcodetrackR" version))
+ (sha256
+ (base32
+ "0yxa15xkgqazw31vq4wm8v747bw4qb18m6i602pvynk0n5bgg3d3"))))
+ (properties `((upstream-name . "barcodetrackR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-circlize
+ r-cowplot
+ r-dplyr
+ r-ggdendro
+ r-ggplot2
+ r-ggridges
+ r-magrittr
+ r-plyr
+ r-proxy
+ r-rcolorbrewer
+ r-rlang
+ r-s4vectors
+ r-scales
+ r-shiny
+ r-summarizedexperiment
+ r-tibble
+ r-tidyr
+ r-vegan
+ r-viridis))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/dunbarlabNIH/barcodetrackR")
+ (synopsis "Functions for analyzing cellular barcoding data")
+ (description
+ "This package is developed for the analysis and visualization of clonal
+tracking data. The required data is formed by samples and tag abundances in
+matrix form, usually from cellular barcoding experiments, integration site
+retrieval analyses, or similar technologies.")
+ (license license:cc0)))
+
(define-public r-biocversion
(package
(name "r-biocversion")
(define-public r-ggcyto
(package
(name "r-ggcyto")
- (version "1.24.0")
+ (version "1.24.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggcyto" version))
(sha256
(base32
- "0sycyvdpa77mykzr709a7padh6478zmnzapibbq90qkc7bxnj359"))))
+ "1cw60x78vqzjmgb5xd3sxyz6zwdaffp3byk34z8d4b3wkh530325"))))
(properties `((upstream-name . "ggcyto")))
(build-system r-build-system)
(propagated-inputs
(define-public r-flowviz
(package
(name "r-flowviz")
- (version "1.60.0")
+ (version "1.60.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowViz" version))
(sha256
(base32
- "175ygncrv6q6mb8pahixs89m9wm6hdpzx489gc9s8lgad2vrvz8f"))))
+ "08rwzc26jns0wwjsqqmf60bpxsckr5x8skdn9iwl8grp81npcc95"))))
(properties `((upstream-name . "flowViz")))
(build-system r-build-system)
(propagated-inputs
(define-public r-flowstats
(package
(name "r-flowstats")
- (version "4.8.0")
+ (version "4.8.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "flowStats" version))
(sha256
(base32
- "1jbc92ah2mlpnd7v3k0207v4qz3rg9g9yy6r6y0s0cc5nifdyhwj"))))
+ "1x01gg5ifxh3wp0cp5a23lr9v6l9q5qg8145q2pgn904jkx5wldc"))))
(properties `((upstream-name . "flowStats")))
(build-system r-build-system)
(propagated-inputs
(define-public r-opencyto
(package
(name "r-opencyto")
- (version "2.8.0")
+ (version "2.8.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "openCyto" version))
(sha256
(base32
- "1nz5fra0jf70jwyfbcz5ksnz5xb62vfnfwfasr0zwwvjvmmvrs1y"))))
+ "0fa3hbbrjw458dhmxdjypcjgyxmphp9kdr3r62qqf803i4wsxfk0"))))
(properties `((upstream-name . "openCyto")))
(build-system r-build-system)
(propagated-inputs
(define-public r-cytoml
(package
(name "r-cytoml")
- (version "2.8.0")
+ (version "2.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "CytoML" version))
(sha256
(base32
- "0vp7advfh1d8596hjpzayasjhga4mx0l104sgz2asscbrjm4v7rr"))))
+ "01yzdljpyq92bv318b5qs29f190226zwbqjnckvxmbb0k8m7s5hw"))))
(properties `((upstream-name . "CytoML")))
(build-system r-build-system)
(inputs
(define-public r-bioccheck
(package
(name "r-bioccheck")
- (version "1.32.0")
+ (version "1.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "BiocCheck" version))
(sha256
(base32
- "1k1gxzmxx26hmwdxgagv93mv4jwyygkk8703ds6nvryzhqffzkbc"))))
+ "0bq4xrz1spp0bmbccxydkw6yw03by5dysz85mn152ab6xixm52lw"))))
(properties
`((upstream-name . "BiocCheck")))
(build-system r-build-system)
(define-public r-biocviews
(package
(name "r-biocviews")
- (version "1.64.0")
+ (version "1.64.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "biocViews" version))
(sha256
(base32
- "1lahla53awdqiglfiygbxg5pkzfabym7n5abgyp1nvqsvsj0g126"))))
+ "0ixcx9qqpmwmnhml3klk5z075km8g2l4q0iqc1dbniga87qgyl38"))))
(properties
`((upstream-name . "biocViews")))
(build-system r-build-system)
(define-public r-biocpkgtools
(package
(name "r-biocpkgtools")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocPkgTools" version))
(sha256
(base32
- "1v0824vmg49q9lh0igdyniryyknw6vmh462rn25kmg9hdna0w99h"))))
+ "0akryshjdn227a8ir8r0lb59v060h58rhy5vjmdxax8p81ajzxkd"))))
(properties `((upstream-name . "BiocPkgTools")))
(build-system r-build-system)
(propagated-inputs
objects from the @code{graph} package.")
(license license:epl1.0)))
+(define-public r-fishpond
+ (package
+ (name "r-fishpond")
+ (version "2.2.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "fishpond" version))
+ (sha256
+ (base32
+ "0svp4yh0srhzbbxy1grchzdd9yzchadjp3d2sy2n9xpwxzpkhrym"))))
+ (properties `((upstream-name . "fishpond")))
+ (build-system r-build-system)
+ (inputs (list zlib))
+ (propagated-inputs
+ (list r-abind
+ r-genomicranges
+ r-gtools
+ r-iranges
+ r-jsonlite
+ r-matrix
+ r-matrixstats
+ r-qvalue
+ r-rcpp
+ r-s4vectors
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-svmisc))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/mikelove/fishpond")
+ (synopsis "Downstream methods and tools for expression data")
+ (description
+ "The @code{fishpond} package contains methods for differential transcript
+and gene expression analysis of RNA-seq data using inferential replicates for
+uncertainty of abundance quantification, as generated by Gibbs sampling or
+bootstrap sampling. Also the package contains a number of utilities for
+working with Salmon and Alevin quantification files.")
+ (license license:gpl2)))
+
(define-public r-fithic
(package
(name "r-fithic")
(define-public r-hdf5array
(package
(name "r-hdf5array")
- (version "1.24.1")
+ (version "1.24.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "HDF5Array" version))
(sha256
(base32
- "1r1lg7k60qgb489xkypd4gvm1fmdlihvylb5va6xj58ipndbfday"))))
+ "1dzx5463ig3ag72a47slc4jbq5id11w77cj0zgzr85h0dbxklrr9"))))
(properties `((upstream-name . "HDF5Array")))
(build-system r-build-system)
(inputs
(define-public r-scuttle
(package
(name "r-scuttle")
- (version "1.6.2")
+ (version "1.6.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scuttle" version))
(sha256
(base32
- "0nnmq3wf436xaw4arc4y3ldvn6ilsg52xzbccmid0icb8z3y2kzn"))))
+ "1w1jy5fqkp2d03lp84d49fsksnl0pcg0wgqyd49d5k1mipdw4671"))))
(properties `((upstream-name . "scuttle")))
(build-system r-build-system)
(propagated-inputs
(define-public r-scran
(package
(name "r-scran")
- (version "1.24.0")
+ (version "1.24.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "scran" version))
(sha256
(base32
- "0xg7dl35915a65pmzkxdacsm4iqf97ayljdjljcvqx1ycmn7x68w"))))
+ "1a6vlq8i5gh7zxm6igmy75187pkx42z28qjag50m49xy5valw3ni"))))
(build-system r-build-system)
(propagated-inputs
(list r-beachmat
(define-public r-delayedmatrixstats
(package
(name "r-delayedmatrixstats")
- (version "1.18.0")
+ (version "1.18.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DelayedMatrixStats" version))
(sha256
(base32
- "1qlwv69c0r2w3zkmsr8r7w6sr3hf1ha0sfcrsjx4ks8f0ww7aqsv"))))
+ "1kq643fmfzq1qjvpj3kc092ahc3qamqgx53layqsyvz5mil55jjv"))))
(properties
`((upstream-name . "DelayedMatrixStats")))
(build-system r-build-system)
(define-public r-pathview
(package
(name "r-pathview")
- (version "1.36.0")
+ (version "1.36.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "pathview" version))
(sha256
- (base32 "1472k107f21cflbx2fip92g8gl9wlwxgwfvgvl73ma0y0jzs0qdq"))))
+ (base32 "11g4zhy4qfq0gmy588334f7s2w1acs2dz9kimax5ya2b8jjibk71"))))
(properties `((upstream-name . "pathview")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bgeecall
(package
(name "r-bgeecall")
- (version "1.12.1")
+ (version "1.12.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BgeeCall" version))
(sha256
(base32
- "1g12cms66zb45p347h3b358vjhnq76galvwqwq86xby4hnwpdzkh"))))
+ "0l6smwy55mm4clb71l4bpch3bayyyf87nq1asbrv6s6fd22mmwil"))))
(properties `((upstream-name . "BgeeCall")))
(build-system r-build-system)
(propagated-inputs
(define-public r-basilisk
(package
(name "r-basilisk")
- (version "1.8.0")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "basilisk" version))
(sha256
(base32
- "1p90wq8a9wrpqpgmcy4zgh5skdw65gg2gsb3lnx78zk9khq0yyzh"))))
+ "134xix2iq5l7783dng2jjklxd3m5lh4snb7bjhslrs2r1j3p8jpk"))))
(properties `((upstream-name . "basilisk")))
(build-system r-build-system)
(propagated-inputs
(define-public r-biocdockermanager
(package
(name "r-biocdockermanager")
- (version "1.8.0")
+ (version "1.8.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BiocDockerManager" version))
(sha256
(base32
- "0kl6r8ad728a8dvqx0safj7v5gj1rxxcdiw44jkr1pd5ddv0xbi6"))))
+ "0a4dcga18bw5mvzmsml28bf4zclz32pp9iflnbvps7pdxvhmmg9d"))))
(properties
`((upstream-name . "BiocDockerManager")))
(build-system r-build-system)
(define-public r-biodb
(package
(name "r-biodb")
- (version "1.4.0")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "biodb" version))
(sha256
(base32
- "02i0n29bp9d9p1ibslxca5m37qsgny2hlgg7d364lf7kc6y2bqni"))))
+ "0f3clqmrpaawhjjyb4x5mnbhsam56r0av05b5cl5p4waylp8qbs1"))))
(properties `((upstream-name . "biodb")))
(build-system r-build-system)
(propagated-inputs
(define-public r-bionero
(package
(name "r-bionero")
- (version "1.4.0")
+ (version "1.4.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "BioNERO" version))
(sha256
(base32
- "1nyzjbl0gcwvbj2nxfwykirikf8j3rsx5ny45bqjbcb4r23k65kj"))))
+ "0dsznfnhidbmf52rv8l26f1ms2k9yy4q4c6cf3x8ylc79c1sjrcp"))))
(properties `((upstream-name . "BioNERO")))
(build-system r-build-system)
(propagated-inputs
(list r-biocparallel
r-complexheatmap
- r-deseq2
r-dynamictreecut
r-genie3
r-ggnetwork
r-ggnewscale
r-ggplot2
- r-ggpubr
+ r-ggrepel
r-igraph
r-intergraph
r-matrixstats
r-minet
r-netrep
r-networkd3
+ r-patchwork
r-rcolorbrewer
r-reshape2
r-summarizedexperiment
visualizing bisulfite sequencing data.")
(license license:artistic2.0)))
+(define-public r-dada2
+ (package
+ (name "r-dada2")
+ (version "1.24.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "dada2" version))
+ (sha256
+ (base32
+ "0nvjnmcjh0i660y8s3rh9b3zl163wxdx7qm2n36m6vf0iy987l4x"))))
+ (properties `((upstream-name . "dada2")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biostrings
+ r-ggplot2
+ r-iranges
+ r-rcpp
+ r-rcppparallel
+ r-reshape2
+ r-shortread
+ r-xvector))
+ (native-inputs (list r-knitr))
+ (home-page "https://benjjneb.github.io/dada2/")
+ (synopsis
+ "Accurate, high-resolution sample inference from amplicon sequencing data")
+ (description
+ "The dada2 package infers exact @dfn{amplicon sequence variants} (ASVs)
+from high-throughput amplicon sequencing data, replacing the coarser and less
+accurate OTU clustering approach. The dada2 pipeline takes as input
+demultiplexed fastq files, and outputs the sequence variants and their
+sample-wise abundances after removing substitution and chimera errors.
+Taxonomic classification is available via a native implementation of the RDP
+naive Bayesian classifier, and species-level assignment to 16S rRNA gene
+fragments by exact matching.")
+ (license license:lgpl2.0)))
+
(define-public r-dmrseq
(package
(name "r-dmrseq")
(define-public r-tximeta
(package
(name "r-tximeta")
- (version "1.14.0")
+ (version "1.14.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "tximeta" version))
(sha256
(base32
- "1vq7x1sf5h8iwdalalbrybxzbq47s2ymb75himj5wkv77mgcivfl"))))
+ "0hxq5lkrdiz0a3xpl88adrv4m55jr6g46a5m9pamc0w4bxddirr8"))))
(properties `((upstream-name . "tximeta")))
(build-system r-build-system)
(propagated-inputs
HCoop / jackhill / guix / guix.git / blobdiff