diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 535 |
1 files changed, 529 insertions, 6 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index b15a856fb9..7ff364ee55 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -68,6 +68,42 @@ ;;; Annotations +(define-public r-bsgenome-hsapiens-ucsc-hg38-masked + (package + (name "r-bsgenome-hsapiens-ucsc-hg38-masked") + (version "1.4.5") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38.masked" version + 'annotation)) + (sha256 + (base32 "0j71hdxqvvc0s8mc6jp6zk502mrf095qazj95yzzb4rm6sjvd20m")))) + (properties `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38.masked"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome r-bsgenome-hsapiens-ucsc-hg38 + r-genomeinfodb)) + (home-page + "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked") + (synopsis + "Full masked genomic sequences for Homo sapiens (UCSC version hg38)") + (description + "This package provides the complete genome sequences for Homo sapiens as +provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). +The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each +of them has the 4 following masks on top: + +@enumerate +@item the mask of assembly gaps (AGAPS mask); +@item the mask of intra-contig ambiguities (AMB mask); +@item the mask of repeats from @code{RepeatMasker} (RM mask); +@item the mask of repeats from Tandem Repeats Finder (TRF mask). +@end enumerate + +Only the AGAPS and AMB masks are \"active\" by default. The sequences are stored +in @code{MaskedDNAString} objects.") + (license license:artistic2.0))) + (define-public r-hpo-db (package (name "r-hpo-db") @@ -507,6 +543,28 @@ Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.") (license license:artistic2.0))) +(define-public r-bsgenome-ecoli-ncbi-20080805 + (package + (name "r-bsgenome-ecoli-ncbi-20080805") + (version "1.3.1000") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BSgenome.Ecoli.NCBI.20080805" version + 'annotation)) + (sha256 + (base32 "1l7mjyys1kaq4mbia9jamyw6sd0ij1wypwxvwy8aksan3gcfnh27")))) + (properties `((upstream-name . "BSgenome.Ecoli.NCBI.20080805"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome)) + (home-page + "https://bioconductor.org/packages/BSgenome.Ecoli.NCBI.20080805") + (synopsis "Escherichia coli full genomes") + (description + "This package provides Escherichia coli full genomes for several strains +as provided by NCBI on 2008/08/05 and stored in Biostrings objects.") + (license license:artistic2.0))) + (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 (package (name "r-bsgenome-hsapiens-1000genomes-hs37d5") @@ -1575,6 +1633,26 @@ biscuiteer.") demonstrate functionalities of the @code{breakpointR} package.") (license license:expat))) +(define-public r-breastcancervdx + (package + (name "r-breastcancervdx") + (version "1.40.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "breastCancerVDX" version + 'experiment)) + (sha256 + (base32 "12r8zql30ssr0cxy8v1qawwsky54321c737ny19n2yrl7sm08gf0")))) + (properties `((upstream-name . "breastCancerVDX"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/breastCancerVDX") + (synopsis "Gene expression datasets") + (description + "This package is a collection of gene expression data from a breast +cancer study published in Wang et al. 2005 and Minn et al 2007.") + (license license:artistic2.0))) + (define-public r-celldex (package (name "r-celldex") @@ -4165,6 +4243,27 @@ 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-bags + (package + (name "r-bags") + (version "2.42.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BAGS" version)) + (sha256 + (base32 "0356ragpcldr48yycqj91sn3bcqvvfp5spv2z02r8g6hs0dndwdh")))) + (properties `((upstream-name . "BAGS"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-breastcancervdx)) + (home-page "https://bioconductor.org/packages/BAGS") + (synopsis "Bayesian approach for geneset selection") + (description + "This R package is providing functions to perform geneset significance +analysis over simple cross-sectional data between 2 and 5 phenotypes of +interest.") + (license license:artistic2.0))) + (define-public r-basespacer (package (name "r-basespacer") @@ -8133,6 +8232,42 @@ nucleotide sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib.") (license license:lgpl2.0+))) +(define-public r-rnbeads + (package + (name "r-rnbeads") + (version "2.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "RnBeads" version)) + (sha256 + (base32 "15z7l4nmpy01xm19717l27nwf3rfsn6wjv211fn2y4ls40mz75qp")))) + (properties `((upstream-name . "RnBeads"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-cluster + r-ff + r-fields + r-genomicranges + r-ggplot2 + r-gplots + r-gridextra + r-illuminaio + r-iranges + r-limma + r-mass + r-matrixstats + r-methylumi + r-plyr + r-s4vectors)) + (home-page "https://bioconductor.org/packages/RnBeads") + (synopsis "RnBeads") + (description + "@code{RnBeads} facilitates comprehensive analysis of various types of DNA +methylation data at the genome scale.") + (license license:gpl3))) + (define-public r-impute (package (name "r-impute") @@ -8637,6 +8772,44 @@ on the basis that cells of the same type should have more similar gene expressio profiles than cells of different types.") (license license:expat))) +(define-public r-methylaid + (package + (name "r-methylaid") + (version "1.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MethylAid" version)) + (sha256 + (base32 "0mzml9j6f7yycf9747ikkpfvxnwji07h8jhwa9a54ix2d0wyxk3d")))) + (properties `((upstream-name . "MethylAid"))) + (build-system r-build-system) + (propagated-inputs + (list r-biobase + r-biocgenerics + r-biocparallel + r-ggplot2 + r-gridbase + r-hexbin + r-matrixstats + r-minfi + r-rcolorbrewer + r-shiny + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://git.bioconductor.org/packages/MethylAid") + (synopsis + "Quality control of large Illumina DNA Methylation array data sets") + (description + "This package provides a visual and interactive web application using +RStudio's shiny package. Bad quality samples are detected using sample-dependent +and sample-independent controls present on the array and user adjustable +thresholds. In depth exploration of bad quality samples can be performed using +several interactive diagnostic plots of the quality control probes present on +the array. Furthermore, the impact of any batch effect provided by the user can +be explored.") + (license license:gpl2+))) + (define-public r-methylkit (package (name "r-methylkit") @@ -9419,6 +9592,37 @@ package contains functions for combining the results of multiple runs of gene set analyses.") (license license:gpl2+))) +(define-public r-powertcr + (package + (name "r-powertcr") + (version "1.22.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "powerTCR" version)) + (sha256 + (base32 "06fmphdq95pjbbvm8m8h1wajbp3vhl0zj7ddbzks9fy7ankp1n3i")))) + (properties `((upstream-name . "powerTCR"))) + (build-system r-build-system) + (propagated-inputs + (list r-cubature + r-doparallel + r-evmix + r-foreach + r-magrittr + r-purrr + r-truncdist + r-vegan + r-vgam)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/powerTCR") + (synopsis "Model-based comparative analysis of the TCR repertoire") + (description + "This package provides a model for the clone size distribution of the +@acronym{TCR, T-cell receptor} repertoire. Further, it permits comparative +analysis of TCR repertoire libraries based on theoretical model fits.") + (license license:artistic2.0))) + ;; This is a CRAN package, but it depends on a Bioconductor package: ;; r-aroma-light, r-dnacopy.. (define-public r-pscbs @@ -10150,6 +10354,49 @@ a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.") (license license:gpl3))) +(define-public r-screpertoire + (package + (name "r-screpertoire") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "scRepertoire" version)) + (sha256 + (base32 "1wgs8dv5zl82iciy86w5ws1gq8v2piklcifbw7gmbw60kijyr2l1")))) + (properties `((upstream-name . "scRepertoire"))) + (build-system r-build-system) + (propagated-inputs + (list r-doparallel + r-dplyr + r-ggalluvial + r-ggplot2 + r-ggraph + r-igraph + r-plyr + r-powertcr + r-reshape2 + r-rlang + r-seuratobject + r-singlecellexperiment + r-stringdist + r-stringr + r-summarizedexperiment + r-tidygraph + r-vegan)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scRepertoire") + (synopsis "Toolkit for single-cell immune receptor profiling") + (description + "The scRepertoire package was built to process data derived from the 10x +Genomics Chromium Immune Profiling for both @acronym{TCR, T-cell receptor} and +@acronym{Ig, immunoglobulin} enrichment workflows and subsequently interacts with +the popular Seurat and SingleCellExperiment R packages. It also allows for +general analysis of single-cell clonotype information without the use of +expression information. The package functions as a wrapper for Startrac and +powerTCR R packages.") + (license license:gpl2))) + (define-public r-scry (package (name "r-scry") @@ -11956,13 +12203,13 @@ rectangular layout tree built by ggtree with the grammar of ggplot2.") (define-public r-ggpicrust2 (package (name "r-ggpicrust2") - (version "1.7.2") + (version "1.7.3") (source (origin (method url-fetch) (uri (cran-uri "ggpicrust2" version)) (sha256 (base32 - "0yk62cc0vmv6dyfiwvvbgpsqlvp1cw61db60153xvzmcdvd077cl")))) + "0zjlsvzl2f74fvqw4ijnai23qwhlcpgd5p8z9dclnwnsgdbm6hcq")))) (properties `((upstream-name . "ggpicrust2"))) (build-system r-build-system) (propagated-inputs (list r-aldex2 @@ -18780,14 +19027,14 @@ using whole genome sequencing data.") (define-public r-activepathways (package (name "r-activepathways") - (version "2.0.2") + (version "2.0.3") (source (origin (method url-fetch) (uri (cran-uri "ActivePathways" version)) (sha256 (base32 - "1h0ih87pf6b5mdhmh65frv3nqx7v5adqv37wn2p3gkpszd6hwc79")))) + "0mgvxpqaq0jncr1kzmwhqkv3pajx2fz6vwhv5arw7fgla6w09p9h")))) (properties `((upstream-name . "ActivePathways"))) (build-system r-build-system) @@ -21782,14 +22029,14 @@ on the plot.") (define-public r-abn (package (name "r-abn") - (version "3.0.2") + (version "3.0.3") (source (origin (method url-fetch) (uri (cran-uri "abn" version)) (sha256 (base32 - "06n69cbkdqpwpxks8276h43132c9v57n4hg33vsjjyxjifwbwxwh")))) + "1yh9nhfphalxh77132r0fkpp71mqsfhb8jk11is4d5nvlvr5316z")))) (build-system r-build-system) (inputs (list gsl)) @@ -22344,6 +22591,122 @@ within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.") (license license:gpl3))) +(define-public r-basic4cseq + (package + (name "r-basic4cseq") + (version "1.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "Basic4Cseq" version)) + (sha256 + (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4")))) + (properties `((upstream-name . "Basic4Cseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-bsgenome-ecoli-ncbi-20080805 + r-catools + r-genomicalignments + r-genomicranges + r-rcircos)) + (home-page "https://bioconductor.org/packages/Basic4Cseq") + (synopsis "Analyzing 4C-seq data") + (description + "Basic4Cseq is an R package for basic filtering, analysis and subsequent +visualization of @acronym{4C-seq, circular chromosome conformation capture +sequencing} data. Virtual fragment libraries can be created for any BSGenome +package, and filter functions for both reads and fragments and basic quality +controls are included. Fragment data in the vicinity of the experiment's +viewpoint can be visualized as a coverage plot based on a running median +approach and a multi-scale contact profile.") + (license license:lgpl3))) + +(define-public r-basics + (package + (name "r-basics") + (version "2.14.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BASiCS" version)) + (sha256 + (base32 "0kf215n151sxphc5w9h4i2xsk7lmysi4abwcpyz4slbwhpki3ac8")))) + (properties `((upstream-name . "BASiCS"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biobase + r-biocgenerics + r-biocparallel + r-coda + r-cowplot + r-ggextra + r-ggplot2 + r-hexbin + r-mass + r-matrix + r-matrixstats + r-posterior + r-rcpp + r-rcpparmadillo + r-reshape2 + r-s4vectors + r-scran + r-scuttle + r-singlecellexperiment + r-summarizedexperiment + r-viridis)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/catavallejos/BASiCS") + (synopsis "Bayesian analysis of single-cell sequencing data") + (description + "@acronym{BASiCS, Bayesian analysis of single-cell sequencing data} is an +integrated Bayesian hierarchical model to perform statistical analyses of +single-cell RNA sequencing datasets in the context of supervised experiments +(where the groups of cells of interest are known a priori. BASiCS performs +built-in data normalisation (global scaling) and technical noise quantification +(based on spike-in genes). BASiCS provides an intuitive detection criterion +for highly (or lowly) variable genes within a single group of cells. +Additionally, BASiCS can compare gene expression patterns between two or more +pre-specified groups of cells.") + (license license:gpl3))) + +(define-public r-basicstarrseq + (package + (name "r-basicstarrseq") + (version "1.30.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BasicSTARRseq" version)) + (sha256 + (base32 "1dw6bv1qk2bn0l3m458sqgvm3s1karh4n3431pl7r0jj2r3mr6xa")))) + (properties `((upstream-name . "BasicSTARRseq"))) + (build-system r-build-system) + (propagated-inputs + (list r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BasicSTARRseq") + (synopsis "Basic peak calling on STARR-seq data") + (description + "This package implements a method that aims to identify enhancers on +large scale. The STARR-seq data consists of two sequencing datasets of the +same targets in a specifc genome. The input sequences show which regions +where tested for enhancers. Significant enriched peaks i.e. a lot more +sequences in one region than in the input where enhancers in the genomic DNA +are, can be identified. So the approach pursued is to call peak every region +in which there is a lot more +(significant in a binomial model) STARR-seq signal than input signal and +propose an enhancer at that very same position. Enhancers then are called +weak or strong dependent of there degree of enrichment in comparison to +input.") + (license license:lgpl3))) + (define-public r-basilisk-utils (package (name "r-basilisk-utils") @@ -22394,6 +22757,166 @@ Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.") (license license:gpl3))) +(define-public r-bayesknockdown + (package + (name "r-bayesknockdown") + (version "1.28.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesKnockdown" version)) + (sha256 + (base32 "1argd4gfld2yb0vvpgb5k7m6agmi58712f6g5dj4gnb7kg4rp1l8")))) + (properties `((upstream-name . "BayesKnockdown"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/BayesKnockdown") + (synopsis "Posterior probabilities for edges from knockdown data") + (description + "This package provides a simple, fast Bayesian method for computing +posterior probabilities for relationships between a single predictor variable +and multiple potential outcome variables, incorporating prior probabilities of +relationships. In the context of knockdown experiments, the predictor +variable is the knocked-down gene, while the other genes are potential +targets. It can also be used for differential expression/2-class data.") + (license license:gpl3))) + +(define-public r-bayesspace + (package + (name "r-bayesspace") + (version "1.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BayesSpace" version)) + (sha256 + (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105")))) + (properties `((upstream-name . "BayesSpace"))) + (build-system r-build-system) + (propagated-inputs + (list r-assertthat + r-biocfilecache + r-biocsingular + r-coda + r-dirichletreg + r-ggplot2 + r-matrix + r-mclust + r-purrr + r-rcpp + r-rcpparmadillo + r-rcppdist + r-rcppprogress + r-rcurl + r-rhdf5 + r-s4vectors + r-scales + r-scater + r-scran + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://www.ezstatconsulting.com/BayesSpace/") + (synopsis "Clustering and resolution enhancement of spatial transcriptomes") + (description + "This package provides tools for clustering and enhancing the resolution +of spatial gene expression experiments. BayesSpace clusters a low-dimensional +representation of the gene expression matrix, incorporating a spatial prior to +encourage neighboring spots to cluster together. The method can enhance the +resolution of the low-dimensional representation into \"sub-spots\", for which +features such as gene expression or cell type composition can be imputed.") + (license license:expat))) + +(define-public r-baynorm + (package + (name "r-baynorm") + (version "1.20.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "bayNorm" version)) + (sha256 + (base32 "01lv4w1x43x3f9sdrqikhsr1gdvkgqzrgcd9wnjj76qsljn57ifq")))) + (properties `((upstream-name . "bayNorm"))) + (build-system r-build-system) + (propagated-inputs + (list r-bb + r-biocparallel + r-dosnow + r-fitdistrplus + r-foreach + r-iterators + r-locfit + r-mass + r-matrix + r-rcpp + r-rcpparmadillo + r-rcppprogress + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/WT215/bayNorm") + (synopsis "Single-cell RNA sequencing data normalization") + (description + "The bayNorm package is used for normalizing single-cell RNA-seq data. +The main function is @code{bayNorm}, which is a wrapper function for gene +specific prior parameter estimation and normalization. The input is a matrix +of scRNA-seq data with rows different genes and coloums different cells. The +output is either point estimates from posterior (2D array) or samples from +posterior (3D array).") + (license license:gpl2+))) + +(define-public r-bbcanalyzer + (package + (name "r-bbcanalyzer") + (version "1.32.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BBCAnalyzer" version)) + (sha256 + (base32 "108jcgsf5hyj348y17hcw8m3zcfjgzpx8nz4n5jgxp2lgxjyizy1")))) + (properties `((upstream-name . "BBCAnalyzer"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-genomicranges + r-iranges + r-rsamtools + r-summarizedexperiment + r-variantannotation)) + (home-page "https://bioconductor.org/packages/BBCAnalyzer") + (synopsis "Visualizing base counts") + (description + "BBCAnalyzer is a package for visualizing the relative or absolute number +of bases, deletions and insertions at defined positions in sequence alignment +data available as bam files in comparison to the reference bases. Markers for +the relative base frequencies, the mean quality of the detected bases, known +mutations or polymorphisms and variants called in the data may additionally be +included in the plots.") + (license license:lgpl3))) + +(define-public r-bcrank + (package + (name "r-bcrank") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "BCRANK" version)) + (sha256 + (base32 "1m1ccacryf8wjzp0d37n9n1kpa6734ddb8nvv1sy0sz5gplrars9")))) + (properties `((upstream-name . "BCRANK"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings)) + (home-page "https://bioconductor.org/packages/BCRANK") + (synopsis "Predicting binding site consensus from ranked DNA sequences") + (description + "This package provides functions and classes for de novo prediction of +transcription factor binding consensus by heuristic search.") + (license license:gpl2))) + (define-public r-biocthis (package (name "r-biocthis") |