;;; Copyright © 2016, 2017, 2018, 2020, 2021 Roel Janssen <roel@gnu.org>
;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl>
;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com>
-;;; Copyright © 2017 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2017, 2022 Efraim Flashner <efraim@flashner.co.il>
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Tobias Geerinckx-Rice <me@tobias.gr>
;;; Copyright © 2019, 2020, 2021, 2022 Simon Tournier <zimon.toutoune@gmail.com>
;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com>
#:use-module (guix git-download)
#:use-module (guix build-system r)
#:use-module (gnu packages)
+ #:use-module (gnu packages autotools)
#:use-module (gnu packages base)
#:use-module (gnu packages bioinformatics)
#:use-module (gnu packages boost)
#:use-module (gnu packages image)
#:use-module (gnu packages maths)
#:use-module (gnu packages netpbm)
+ #:use-module (gnu packages python)
#:use-module (gnu packages perl)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages statistics)
from Illumina 450k methylation arrays.")
(license license:artistic2.0)))
+(define-public r-bladderbatch
+ (package
+ (name "r-bladderbatch")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "bladderbatch" version
+ 'experiment))
+ (sha256
+ (base32
+ "1dpbaqsqizyi99r0imf5m4lndhhrkyiaqii9bi8rp18fjbjdd72k"))))
+ (properties `((upstream-name . "bladderbatch")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase))
+ (home-page "https://bioconductor.org/packages/bladderbatch")
+ (synopsis "Bladder gene expression data illustrating batch effects")
+ (description
+ "This package contains microarray gene expression data on 57 bladder samples from
+5 batches. The data are used as an illustrative example for the sva package.")
+ (license license:artistic2.0)))
+
(define-public r-biscuiteerdata
(package
(name "r-biscuiteerdata")
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")
across the entire multi-'omics experiment.")
(license license:artistic2.0)))
+(define-public r-parathyroidse
+ (package
+ (name "r-parathyroidse")
+ (version "1.34.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "parathyroidSE" version
+ 'experiment))
+ (sha256
+ (base32
+ "1h33x55c4gbzmh085skqif04wdcvjp2l9fm55qzwws27kwd30c16"))))
+ (properties `((upstream-name . "parathyroidSE")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-summarizedexperiment))
+ (home-page "https://bioconductor.org/packages/parathyroidSE")
+ (synopsis "RangedSummarizedExperiment for RNA-Seq of parathyroid tumors")
+ (description
+ "This package provides @code{RangedSummarizedExperiment} objects of read
+counts in genes and exonic parts for paired-end RNA-Seq data from experiments on
+primary cultures of parathyroid tumors. The sequencing was performed on tumor
+cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control).")
+ ;; The author(s) mentions only LGPL without any specific version.
+ (license license:lgpl2.1+)))
+
(define-public r-tcgabiolinksgui-data
(package
(name "r-tcgabiolinksgui-data")
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
(description
"The project is intended to support the use of @dfn{sequins}(synthetic
sequencing spike-in controls) owned and made available by the Garvan Institute
-of Medical Research. The goal is to provide a standard open source library for
-quantitative analysis, modelling and visualization of spike-in controls.")
+of Medical Research. The goal is to provide a standard library for quantitative
+analysis, modelling, and visualization of spike-in controls.")
(license license:bsd-3)))
(define-public r-aneufinder
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-dearseq
(package
(name "r-dearseq")
- (version "1.8.1")
+ (version "1.8.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "dearseq" version))
(sha256
(base32
- "1f144k5gsclcmsnlsbisr2mivk91dbkci83wx1kznw6i15p4cpj1"))))
+ "1zsqsgf243gq1k57mw11d6apzccnq531mwg2wzw9mjrs1m0jsfzl"))))
(build-system r-build-system)
(propagated-inputs
(list r-compquadform
arbitrary genomic intervals along chromosomal ideogram.")
(license license:gpl2)))
+(define-public r-infercnv
+ (package
+ (name "r-infercnv")
+ (version "1.12.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "infercnv" version))
+ (sha256
+ (base32
+ "01f021fdxm058733rky46dlvqg7dmf5mn5x9lnq0fspp5665w3bl"))))
+ (properties `((upstream-name . "infercnv")))
+ (build-system r-build-system)
+ (inputs (list python))
+ (propagated-inputs
+ (list r-ape
+ r-argparse
+ r-biocgenerics
+ r-catools
+ r-coda
+ r-coin
+ r-digest
+ r-doparallel
+ r-dplyr
+ r-edger
+ r-fastcluster
+ r-fitdistrplus
+ r-foreach
+ r-futile-logger
+ r-future
+ r-ggplot2
+ r-gplots
+ r-gridextra
+ r-hiddenmarkov
+ r-leiden
+ r-matrix
+ r-paralleldist
+ r-phyclust
+ r-rann
+ r-rcolorbrewer
+ r-reshape
+ r-rjags
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/broadinstitute/inferCNV/wiki")
+ (synopsis "Infer copy number variation from single-cell RNA-Seq data")
+ (description
+ "@code{InferCNV} is used to explore tumor single cell RNA-Seq data to identify
+evidence for somatic large-scale chromosomal copy number alterations, such as gains
+or deletions of entire chromosomes or large segments of chromosomes. This is done
+by exploring expression intensity of genes across positions of a tumor genome in
+comparison to a set of reference \"normal\" cells. A heatmap is generated
+illustrating the relative expression intensities across each chromosome, and it
+often becomes readily apparent as to which regions of the tumor genome are
+over-abundant or less-abundant as compared to that of normal cells.")
+ (license license:bsd-3)))
+
(define-public r-iranges
(package
(name "r-iranges")
- (version "2.30.0")
+ (version "2.30.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "IRanges" version))
(sha256
(base32
- "0hfx5n0b4pqrrc1w2dik596803ly8ffnxfs768iy5l5kr8wwyc8k"))))
+ "1r01c9lczkchgd9hbxxd6wrd5avhy52mfqjck7l9avjq1jimvzv3"))))
(properties
`((upstream-name . "IRanges")))
(build-system r-build-system)
(define-public r-annotationforge
(package
(name "r-annotationforge")
- (version "1.38.0")
+ (version "1.38.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "AnnotationForge" version))
(sha256
(base32
- "18rcfadxdaggyjj3rj17nbvgddlqs6zlr5jmq9a02kin59czvzz8"))))
+ "0lcr79a3570h7zg4z691gxg2vlyqnars5811q0clzinbmq7b4x3v"))))
(properties
`((upstream-name . "AnnotationForge")))
(build-system r-build-system)
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")
(define-public r-biostrings
(package
(name "r-biostrings")
- (version "2.64.0")
+ (version "2.64.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "Biostrings" version))
(sha256
(base32
- "1sz52hz89l9w2y2bvyis7kczslk1xnskls9l2bn1s3dhnjzdzhg8"))))
+ "1wk8nlmp6f6fsjrcb4fb48s3ay38yywwad748i6lfkkcw2pdfw33"))))
(properties
`((upstream-name . "Biostrings")))
(build-system r-build-system)
(define-public r-chipseeker
(package
(name "r-chipseeker")
- (version "1.32.0")
+ (version "1.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "ChIPseeker" version))
(sha256
(base32
- "001f85nk4myk9vgs05inlj2dfby4802p1iyzkfqg332yk52gsbl7"))))
+ "0l2514wvlc8q7n1zjzfrghdg372sp73z39204bkif3g6pdkcvbcf"))))
(build-system r-build-system)
(native-inputs
(list r-knitr))
r-genomicranges
r-genomicfeatures
r-ggplot2
+ r-ggvenndiagram
r-gplots
r-gtools
r-dplyr
(define-public r-complexheatmap
(package
(name "r-complexheatmap")
- (version "2.12.0")
+ (version "2.12.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ComplexHeatmap" version))
(sha256
(base32
- "15b49vlkl89prcw70mlw066z0gxhs26x8dpfn6qr3gz7hihygs65"))))
+ "0b4p3ijhdcydfp0j58xlb5dn7d3m2x420n91rl9diqpg4r2gl0s8"))))
(properties
`((upstream-name . "ComplexHeatmap")))
(build-system r-build-system)
(define-public r-edger
(package
(name "r-edger")
- (version "3.38.1")
+ (version "3.38.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "edgeR" version))
(sha256
(base32
- "1q933m76155gy30wgps2gdd8pxzsfhppydjqn0fhjrwj6kqz8mik"))))
+ "1ww69xrg9qrmq7dix2k48j6akgn58ss3340hm7pjvzx508x1j6n6"))))
(properties `((upstream-name . "edgeR")))
(build-system r-build-system)
(propagated-inputs
- (list r-limma r-locfit r-rcpp r-statmod)) ;for estimateDisp
+ (list r-limma r-locfit r-rcpp))
(home-page "http://bioinf.wehi.edu.au/edgeR")
(synopsis "EdgeR does empirical analysis of digital gene expression data")
(description "This package can do differential expression analysis of
(define-public r-gage
(package
(name "r-gage")
- (version "2.46.0")
+ (version "2.46.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "gage" version))
(sha256
(base32
- "03hx188h98qrbpjlf8v9sg2vqyfv49rp4c18ir11pg6hwqqrxh7b"))))
+ "01y04jcy7a9fksyhj0nq37n1inkrpqf4qv117lflvipbx0dsw4gl"))))
(build-system r-build-system)
(propagated-inputs
(list r-annotationdbi r-go-db r-graph r-keggrest))
(define-public r-genomeinfodb
(package
(name "r-genomeinfodb")
- (version "1.32.2")
+ (version "1.32.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomeInfoDb" version))
(sha256
(base32
- "1n37bwb2fqmdgqbn19rgsd2qn8vbdhv6khdwjr7v12bwabcbx9xh"))))
+ "0z2bqr0zrl3r2kcqs72ny8p1psf8w1sgbr7qjjknxdv1qp8m2j7v"))))
(properties
`((upstream-name . "GenomeInfoDb")))
(build-system r-build-system)
(define-public r-genomicalignments
(package
(name "r-genomicalignments")
- (version "1.32.0")
+ (version "1.32.1")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicAlignments" version))
(sha256
(base32
- "1ifmlc0488f5yzcf4p92dmdc7psxl5c0aa7qpxjk0a07gf7lldbi"))))
+ "09pg7822camyav5zvlpv360sj5gz8q1bhk528qa2da2qsz74a3cz"))))
(properties
`((upstream-name . "GenomicAlignments")))
(build-system r-build-system)
(define-public r-genomicfeatures
(package
(name "r-genomicfeatures")
- (version "1.48.3")
+ (version "1.48.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "GenomicFeatures" version))
(sha256
(base32
- "0f14p1ma2y8l60p9sxmh5j0axws9by1cznczb2jxipphpb4slpl1"))))
+ "15kn5lmdqp7rsh2zlixj7ashsqnv50bs36hapw36qbaz9vgvim4v"))))
(properties
`((upstream-name . "GenomicFeatures")))
(build-system r-build-system)
(define-public r-keggrest
(package
(name "r-keggrest")
- (version "1.36.2")
+ (version "1.36.3")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "KEGGREST" version))
(sha256
(base32
- "1rn03w8y80prbvzahkvf8275haiymnjj1ijcgn55p3d0sb54yzgw"))))
+ "0lzb3z6pzm323q70931b7220ygml7jb4g81dybwa79wqiqz15pni"))))
(properties `((upstream-name . "KEGGREST")))
(build-system r-build-system)
(propagated-inputs
(define-public r-limma
(package
(name "r-limma")
- (version "3.52.2")
+ (version "3.52.4")
(source (origin
(method url-fetch)
(uri (bioconductor-uri "limma" version))
(sha256
(base32
- "0m8p8pqmf48f2zdf3qs66hmychbc58g2hfg1wyxzsv180m6xkk65"))))
+ "14xy3qyra2crz31sxgz768mhnhhvcpfhfcigf4xsii643lqcz75h"))))
(build-system r-build-system)
(home-page "http://bioinf.wehi.edu.au/limma")
(synopsis "Package for linear models for microarray and RNA-seq data")
different technologies, including microarrays, RNA-seq, and quantitative PCR.")
(license license:gpl2+)))
+(define-public r-made4
+ (package
+ (name "r-made4")
+ (version "1.70.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "made4" version))
+ (sha256
+ (base32
+ "1wrv9d2mp799qzy1bsaj4w7wx12gdhfv9qvklz7z41vfz59d6bq5"))))
+ (properties `((upstream-name . "made4")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-ade4
+ r-biobase
+ r-gplots
+ r-rcolorbrewer
+ r-scatterplot3d
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "http://www.hsph.harvard.edu/aedin-culhane/")
+ (synopsis "Multivariate analysis of microarray data using ADE4")
+ (description
+ "This is a package for multivariate data analysis and graphical display
+of microarray data. Functions are included for supervised dimension
+reduction (between group analysis) and joint dimension reduction of two
+datasets (coinertia analysis).")
+ (license license:artistic2.0)))
+
(define-public r-methylkit
(package
(name "r-methylkit")
throughput genetic sequencing data sets using regression methods.")
(license license:artistic2.0)))
+(define-public r-muscat
+ (package
+ (name "r-muscat")
+ (version "1.10.1")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "muscat" version))
+ (sha256
+ (base32
+ "1j3zkhqgza92vdykb1yia1jjwsdqra6q9c0jk6p5p2x0778xqgfd"))))
+ (properties `((upstream-name . "muscat")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocparallel
+ r-blme
+ r-complexheatmap
+ r-data-table
+ r-deseq2
+ r-dplyr
+ r-edger
+ r-ggplot2
+ r-glmmtmb
+ r-limma
+ r-lme4
+ r-lmertest
+ r-matrix
+ r-matrixstats
+ r-progress
+ r-purrr
+ r-s4vectors
+ r-scales
+ r-scater
+ r-sctransform
+ r-scuttle
+ r-singlecellexperiment
+ r-summarizedexperiment
+ r-variancepartition
+ r-viridis))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/HelenaLC/muscat")
+ (synopsis "Multi-sample multi-group scRNA-seq data analysis tools")
+ (description
+ "This package @code{muscat} provides various methods and visualization tools
+for @dfn{DS}(differential splicing) analysis in multi-sample, multi-group,
+multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and
+methods based on aggregated \"pseudobulk\" data, as well as a flexible simulation
+platform that mimics both single and multi-sample scRNA-seq data.")
+ (license license:gpl3)))
+
(define-public r-mutationalpatterns
(package
(name "r-mutationalpatterns")
previously been used in XCMS.")
(license license:artistic2.0)))
+(define-public r-organism-dplyr
+ (package
+ (name "r-organism-dplyr")
+ (version "1.24.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "Organism.dplyr" version))
+ (sha256
+ (base32
+ "0j29f85d66c45ww3417xx376vpz0mmvga5n7h2cl1sd4h70b55as"))))
+ (properties `((upstream-name . "Organism.dplyr")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-annotationfilter
+ r-biocfilecache
+ r-dbi
+ r-dbplyr
+ r-dplyr
+ r-genomeinfodb
+ r-genomicfeatures
+ r-genomicranges
+ r-iranges
+ r-rlang
+ r-rsqlite
+ r-s4vectors
+ r-tibble))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/Organism.dplyr")
+ (synopsis "Dplyr-based access to Bioconductor annotation resources")
+ (description
+ "This package provides an alternative interface to Bioconductor @code{
+annotation} resources, in particular the gene identifier mapping functionality
+of the @code{org} packages (e.g., @code{org.Hs.eg.db}) and the genome coordinate
+functionality of the @code{TxDb} packages (e.g.,
+@code{TxDb.Hsapiens.UCSC.hg38.knownGene}).")
+ (license license:artistic2.0)))
+
(define-public r-organismdbi
(package
(name "r-organismdbi")
the fact that each of these packages implements a select methods.")
(license license:artistic2.0)))
+(define-public r-pcaexplorer
+ (package
+ (name "r-pcaexplorer")
+ (version "2.22.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "pcaExplorer" version))
+ (sha256
+ (base32
+ "0xkafpi6y5n8hljdaj183hd5z4ik7lpbklg2cbx1hwfz4n4hh1bl"))))
+ (properties `((upstream-name . "pcaExplorer")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-annotationdbi
+ r-base64enc
+ r-biomart
+ r-deseq2
+ r-dt
+ r-genefilter
+ r-genomicranges
+ r-ggplot2
+ r-ggrepel
+ r-go-db
+ r-gostats
+ r-heatmaply
+ r-iranges
+ r-knitr
+ r-limma
+ r-nmf
+ r-pheatmap
+ r-plotly
+ r-plyr
+ r-rmarkdown
+ r-s4vectors
+ r-scales
+ r-shiny
+ r-shinyace
+ r-shinybs
+ r-shinydashboard
+ r-summarizedexperiment
+ r-threejs
+ r-tidyr
+ r-topgo))
+ (native-inputs (list r-knitr))
+ (home-page "https://github.com/federicomarini/pcaExplorer")
+ (synopsis
+ "Interactive Visualization of RNA-seq Data Using a Principal Components Approach")
+ (description
+ "This package provides functionality for interactive visualization of RNA-seq
+datasets based on Principal Components Analysis. The methods provided allow for
+quick information extraction and effective data exploration. A Shiny
+application encapsulates the whole analysis.")
+ (license license:expat)))
+
(define-public r-pcamethods
(package
(name "r-pcamethods")
different experiment.")
(license license:gpl3)))
+(define-public r-scry
+ (package
+ (name "r-scry")
+ (version "1.8.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "scry" version))
+ (sha256
+ (base32
+ "16mj21r91jy8ircdz8rfrdli9gjy0hrx90kf6ghs305d3d4dl193"))))
+ (properties `((upstream-name . "scry")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocsingular
+ r-delayedarray
+ r-glmpca
+ r-hdf5array
+ r-matrix
+ r-singlecellexperiment
+ r-summarizedexperiment))
+ (native-inputs (list r-knitr))
+ (home-page "https://bioconductor.org/packages/scry.html")
+ (synopsis "Small-count analysis methods for high-dimensional data")
+ (description
+ "Many modern biological datasets consist of small counts that are not
+well fit by standard linear-Gaussian methods such as principal component
+analysis. This package provides implementations of count-based feature
+selection and dimension reduction algorithms. These methods can be used to
+facilitate unsupervised analysis of any high-dimensional data such as
+single-cell RNA-seq.")
+ (license license:artistic2.0)))
+
(define-public r-seqlogo
(package
(name "r-seqlogo")
(define-public r-valr
(package
(name "r-valr")
- (version "0.6.4")
+ (version "0.6.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "valr" version))
(sha256
(base32
- "0dd41irvibh6rwi52bw4zg4m7wpyihlp1kdkb8fdji3csw2fiz4k"))))
+ "1674sqclgi4l5r544pjjsblzl1ix2cy961jpkncb3ym47y6c1msw"))))
(build-system r-build-system)
(propagated-inputs
(list r-broom
(define-public r-zellkonverter
(package
(name "r-zellkonverter")
- (version "1.6.3")
+ (version "1.6.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "zellkonverter" version))
(sha256
- (base32 "0l6v7a2zyxpq2w3vm85z439ldi3ld3pkc3wx95a1vxzbr31cpdzz"))))
+ (base32 "0rxpjkisjj1xjchjjm72k8za5hn48wbdahmbllljvxm5ii6k36k6"))))
(properties `((upstream-name . "zellkonverter")))
(build-system r-build-system)
(propagated-inputs
`(("r-knitr" ,r-knitr)))
(home-page "https://github.com/yixuan/RcppNumerical")
(synopsis "Rcpp integration for numerical computing libraries")
- (description "This package provides a collection of open source libraries
-for numerical computing (numerical integration, optimization, etc.) and their
-integration with @code{Rcpp}.")
+ (description
+ "This package provides a collection of libraries for numerical computing
+(numerical integration, optimization, etc.) and their integration with
+@code{Rcpp}.")
(license license:gpl2+)))
(define-public r-apeglm
(define-public r-diffbind
(package
(name "r-diffbind")
- (version "3.6.1")
+ (version "3.6.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DiffBind" version))
(sha256
(base32
- "0izlk8vmmal4dj0bjxhgzr25arfa9zgdv06rm70w7ylr0gl84pzr"))))
+ "035xczcir4q7yj6x9m3yq3dpvbfas9la925avni8147cwhybagqr"))))
(properties `((upstream-name . "DiffBind")))
(build-system r-build-system)
(propagated-inputs
(define-public r-perfmeas
(package
(name "r-perfmeas")
- (version "1.2.1")
+ (version "1.2.5")
(source
(origin
(method url-fetch)
(uri (cran-uri "PerfMeas" version))
(sha256
(base32
- "1x7ancmb41zd1js24rx94plgbssyc71z2bvpic6mg34xjkwdjw93"))))
+ "13yjk0kwpbsqwl056hzf0zj2br1mk4faqcn1whdfxmq348c14hjb"))))
(properties `((upstream-name . "PerfMeas")))
(build-system r-build-system)
(propagated-inputs
(define-public r-scaledmatrix
(package
(name "r-scaledmatrix")
- (version "1.4.0")
+ (version "1.4.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ScaledMatrix" version))
(sha256
(base32
- "0p6065mbn77hphpjfchz3r3raspl127f11n39mwh9bih4zg375cl"))))
+ "05gxr41nb1jqhv357rfha4062kszvrmkr36mhkjsf7kgnzf0p8hz"))))
(properties `((upstream-name . "ScaledMatrix")))
(build-system r-build-system)
(propagated-inputs
(define-public r-treeio
(package
(name "r-treeio")
- (version "1.20.0")
+ (version "1.20.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "treeio" version))
(sha256
(base32
- "1hc5m0b2qqxrh3z0inny2jizrpn9d4yn9pn3k1h18xb4ggyijyla"))))
+ "1jymbyl82n88ckw0nkbj72rvlxbk5m7xmcmq3fyi885z7aasc0x1"))))
(properties `((upstream-name . "treeio")))
(build-system r-build-system)
(propagated-inputs
(define-public r-ggtree
(package
(name "r-ggtree")
- (version "3.4.0")
+ (version "3.4.4")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ggtree" version))
(sha256
(base32
- "033r748npv0l72yb9sk6lqnj0l7cd36ykf788145qv8ck5i2gyk4"))))
+ "0h1qlhn4rj7jgd9vrja7lykaglyfvnzwkghvsqj1mvp4niwli7y5"))))
(properties `((upstream-name . "ggtree")))
(build-system r-build-system)
(propagated-inputs
(define-public r-htscluster
(package
(name "r-htscluster")
- (version "2.0.8")
+ (version "2.0.10")
(source
(origin
(method url-fetch)
(uri (cran-uri "HTSCluster" version))
(sha256
(base32
- "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
+ "0scn4fsfmlkzxibfhsh6krm2cl9c8hsmyjgn48k9dyjf0ylyxg9n"))))
(properties `((upstream-name . "HTSCluster")))
(build-system r-build-system)
(propagated-inputs
(base32
"0kc708ss5byzw8qh439mb4nq6hsfmz73gfamiznw3lv352brd33g"))))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'make-build-order-reproducible
+ (lambda _
+ (substitute* '("src/SYMPHONY/Cgl/configure.ac"
+ "src/SYMPHONY/Cgl/configure")
+ (("for file in `ls \\*/Makefile.in`")
+ "for file in `ls */Makefile.in | sort`")))))))
(inputs
(list zlib))
(native-inputs
(define-public r-residualmatrix
(package
(name "r-residualmatrix")
- (version "1.6.0")
+ (version "1.6.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ResidualMatrix" version))
(sha256
(base32
- "1pjr3gva0jwj2pgqr4k4nl1ir1153hhrk1d400r30w0di472hns4"))))
+ "1530706c7b53h9m8smgnaj63rgdbm3hd09n7jwy6zc0y6qcffckd"))))
(properties
`((upstream-name . "ResidualMatrix")))
(build-system r-build-system)
studies.")
(license license:artistic2.0)))
+(define-public r-milor
+ (package
+ (name "r-milor")
+ (version "1.4.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "miloR" version))
+ (sha256
+ (base32
+ "1jz9p3grnczx0bpdw6j64x21in8zgm3qy19hmm296har2rx9m5zs"))))
+ (properties `((upstream-name . "miloR")))
+ (build-system r-build-system)
+ (propagated-inputs
+ (list r-biocgenerics
+ r-biocneighbors
+ r-biocparallel
+ r-biocsingular
+ r-cowplot
+ r-dplyr
+ r-edger
+ r-ggbeeswarm
+ r-ggplot2
+ r-ggraph
+ r-ggrepel
+ r-gtools
+ r-igraph
+ r-irlba
+ r-limma
+ r-matrix
+ r-matrixstats
+ r-patchwork
+ r-rcolorbrewer
+ r-s4vectors
+ r-singlecellexperiment
+ r-stringr
+ r-summarizedexperiment
+ r-tibble
+ r-tidyr))
+ (native-inputs (list r-knitr))
+ (home-page "https://marionilab.github.io/miloR")
+ (synopsis "Differential neighbourhood abundance testing on a graph")
+ (description
+ "Milo performs single-cell differential abundance testing. Cell states
+are modelled as representative neighbourhoods on a nearest neighbour graph.
+Hypothesis testing is performed using a negative bionomial generalized linear
+model.")
+ (license license:gpl3)))
+
(define-public r-minfi
(package
(name "r-minfi")
the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively
involved in translation (the actively translating mRNA level) for each mRNA.
The standard analysis of such data strives towards identifying differential
-translational between two or more sample classes - i.e. differences in
+translational between two or more sample classes - i.e., differences in
actively translated mRNA levels that are independent of underlying differences
in cytosolic mRNA levels. This package allows for such analysis using partial
variances and the random variance model. As 10s of thousands of mRNAs are
(define-public r-dose
(package
(name "r-dose")
- (version "3.22.0")
+ (version "3.22.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "DOSE" version))
(sha256
(base32
- "11lg4ql0bi54p2wg3z1dw9rwqai37khgcqbs4cb7zf67ml8jadwp"))))
+ "1mch26kddrhhzgi4bssnyy7bvdhprrncmvxl6zn1cq7g07p5765i"))))
(properties `((upstream-name . "DOSE")))
(build-system r-build-system)
(propagated-inputs
(define-public r-enrichplot
(package
(name "r-enrichplot")
- (version "1.16.1")
+ (version "1.16.2")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "enrichplot" version))
(sha256
(base32
- "17ln1wbkq8sp7jw0dpkccj5qcsl382sgd7zic04dk99z9ag3mh02"))))
+ "0qh7bci3rn6y2fl45izrdb62jcm6j0zxxg4pyp4mvvgjvka5lnss"))))
(build-system r-build-system)
(propagated-inputs
(list r-aplot
(define-public r-rgadem
(package
(name "r-rgadem")
- (version "2.44.0")
+ (version "2.44.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "rGADEM" version))
(sha256
(base32
- "013xdwz0c3n0n9hxf8kkx570qry961pgdjsp023531pl5ww2ing4"))))
+ "052z9iavnmkaz9jzz7ycpb8z7qqq3s5k6a04icrwl00wff7zqa2q"))))
(properties `((upstream-name . "rGADEM")))
(build-system r-build-system)
(propagated-inputs
(define-public r-rsubread
(package
(name "r-rsubread")
- (version "2.10.4")
+ (version "2.10.5")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "Rsubread" version))
(sha256
(base32
- "155h25gbagqns7wpriil17li0jkdd1z1pcz0dlnikdqj4saf97rl"))))
+ "0n9qqbkj2lgxkia6kfpfz06wbc1lvw24qyvn88f48zw5nh0rsrs2"))))
(properties `((upstream-name . "Rsubread")))
(build-system r-build-system)
(inputs (list zlib))
(define-public r-ncdfflow
(package
(name "r-ncdfflow")
- (version "2.42.0")
+ (version "2.42.1")
(source
(origin
(method url-fetch)
(uri (bioconductor-uri "ncdfFlow" version))
(sha256
(base32
- "18ba8rygcd1ys150pk38r4w5lxwm6sl76zkd294yg847dygsqa4m"))))
+ "0759xvkp22dnbhq5wpgvpk8p61w0d50r5jrbh9n7sj8sga4lvvv7"))))
(properties `((upstream-name . "ncdfFlow")))
(build-system r-build-system)
(propagated-inputs
(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
"This package provides a pipeline for analysing Capture Hi-C data.")
(license license:artistic2.0)))
+;; This is a CRAN package, but it depends on Bioconductor packages, so we put
+;; it here.
+(define-public r-ciara
+ (package
+ (name "r-ciara")
+ (version "0.1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (cran-uri "CIARA" version))
+ (sha256
+ (base32
+ "0nr7wks9231326x0lhpbh824c6vcb5hr5jn89s9bmg9mci907bsf"))))
+ (properties `((upstream-name . "CIARA")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-biobase r-ggplot2 r-ggraph r-magrittr))
+ (native-inputs (list r-knitr))
+ (home-page "https://cran.r-project.org/package=CIARA")
+ (synopsis "Cluster-independent algorithm for rare cell types identification")
+ (description
+ "This is a package to support identification of markers of rare cell
+types by looking at genes whose expression is confined in small regions of the
+expression space.")
+ (license license:artistic2.0)))
+
(define-public r-cicero
(package
(name "r-cicero")
(define-public r-activedriverwgs
(package
(name "r-activedriverwgs")
- (version "1.1.2")
+ (version "1.2.0")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActiveDriverWGS" version))
(sha256
(base32
- "13b5yazgv9kckcp6gck183mh1m0q8lc5ixagmcy9s8kv2wz7wq45"))))
+ "0xnplgwxd197a4d422bsxg753q158i12ils16awd1cw30wafdxkk"))))
(properties
`((upstream-name . "ActiveDriverWGS")))
(build-system r-build-system)
(define-public r-activepathways
(package
(name "r-activepathways")
- (version "1.1.0")
+ (version "1.1.1")
(source
(origin
(method url-fetch)
(uri (cran-uri "ActivePathways" version))
(sha256
(base32
- "0zbrgz91mlik7j8j11wsdswqqqfsijj8jkgd5fx1ar3mc6rqsmbg"))))
+ "1crq164vyqhdq5y3q09k3m5zljqrhcd5ak0jrc0xqvzf0pasml2m"))))
(properties
`((upstream-name . "ActivePathways")))
(build-system r-build-system)
"0q2y4n6bcc9pvz5sgfkw1lrb00rrp7q29i1vh7srdfmfhgpyz6bk"))))
(properties `((upstream-name . "bgx")))
(build-system r-build-system)
+ (arguments
+ (list
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'do-not-tune-cflags-for-reproducibility
+ (lambda _
+ (substitute* "configure.ac"
+ (("AX_GCC_ARCHFLAG.*") ""))
+ (delete-file "configure")
+ (invoke "autoreconf" "-vif"))))))
+ (inputs
+ (list boost))
(propagated-inputs
(list r-affy r-biobase r-gcrma r-rcpp))
+ (native-inputs
+ (list autoconf automake))
(home-page "https://bioconductor.org/packages/bgx/")
(synopsis "Bayesian gene expression")
(description
(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")
interest on transformed methylation proportions.")
(license license:expat)))
+(define-public r-omicade4
+ (package
+ (name "r-omicade4")
+ (version "1.36.0")
+ (source (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "omicade4" version))
+ (sha256
+ (base32
+ "1l7w3sczsimg640klq8navgdcwjj090wjqd40n4mw76pny2xj2lj"))))
+ (properties `((upstream-name . "omicade4")))
+ (build-system r-build-system)
+ (propagated-inputs (list r-ade4 r-biobase r-made4))
+ (home-page "https://bioconductor.org/packages/omicade4")
+ (synopsis "Multiple co-inertia analysis of omics datasets")
+ (description
+ "This package performes multiple co-inertia analysis of omics datasets.")
+ (license license:gpl2)))
+
(define-public r-omnipathr
(package
(name "r-omnipathr")
(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
"Phyloseq provides a set of classes and tools to facilitate the import,
storage, analysis, and graphical display of microbiome census data.")
(license license:agpl3)))
+
+;;;
+;;; Avoid adding new packages to the end of this file. To reduce the chances
+;;; of a merge conflict, place them above by existing packages with similar
+;;; functionality or similar names.
+;;;
HCoop / jackhill / guix / guix.git / blobdiff