;;; 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)
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
(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)
(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")
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")
(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
(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)
"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