diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 956 |
1 files changed, 847 insertions, 109 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index bc8eda4293..d9d9274095 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -1436,51 +1436,6 @@ curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.") (license license:gpl3))) -(define-public r-cellid - (package - (name "r-cellid") - (version "1.8.1") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "CelliD" version)) - (sha256 - (base32 - "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) - (properties `((upstream-name . "CelliD"))) - (build-system r-build-system) - (propagated-inputs - (list r-data-table - r-biocparallel - r-fastmatch - r-fgsea - r-ggplot2 - r-glue - r-irlba - r-matrix - r-matrixstats - r-pbapply - r-rcpp - r-rcpparmadillo - r-reticulate - r-rtsne - r-seurat - r-stringr - r-tictoc - r-singlecellexperiment - r-summarizedexperiment - r-umap)) - (native-inputs (list r-knitr r-scater)) - (home-page "https://bioconductor.org/packages/CelliD") - (synopsis - "Single cell gene signature extraction using multiple correspondence analysis") - (description - "CelliD is a clustering-free method for extracting per-cell gene -signatures from scRNA-seq. CelliD allows unbiased cell identity recognition -across different donors, tissues-of-origin, model organisms and single-cell -omics protocols. The package can also be used to explore functional pathways -enrichment in single cell data.") - (license license:gpl3))) - (define-public r-champdata (package (name "r-champdata") @@ -1776,56 +1731,6 @@ in Nature Genetics, January 2018.") methylation arrays.") (license license:artistic2.0))) -(define-public r-missmethyl - (package - (name "r-missmethyl") - (version "1.34.0") - (source (origin - (method url-fetch) - (uri (bioconductor-uri "missMethyl" version)) - (sha256 - (base32 - "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h")))) - (properties `((upstream-name . "missMethyl"))) - (build-system r-build-system) - (propagated-inputs - (list r-annotationdbi - r-biasedurn - r-biobase - r-biocgenerics - r-genomicranges - r-go-db - r-illuminahumanmethylation450kanno-ilmn12-hg19 - r-illuminahumanmethylation450kmanifest - r-illuminahumanmethylationepicanno-ilm10b4-hg19 - r-illuminahumanmethylationepicmanifest - r-iranges - r-limma - r-methylumi - r-minfi - r-org-hs-eg-db - r-ruv - r-s4vectors - r-statmod - r-stringr - r-summarizedexperiment)) - (native-inputs (list r-knitr)) - (home-page "https://bioconductor.org/packages/missMethyl") - (synopsis "Analyzing Illumina HumanMethylation BeadChip data") - (description - "This is a package for normalization, testing for differential -variability and differential methylation and gene set testing for data from -Illumina's Infinium HumanMethylation arrays. The normalization procedure is -subset-quantile within-array normalization (SWAN), which allows Infinium I and -II type probes on a single array to be normalized together. The test for -differential variability is based on an empirical Bayes version of Levene's -test. Differential methylation testing is performed using RUV, which can -adjust for systematic errors of unknown origin in high-dimensional data by -using negative control probes. Gene ontology analysis is performed by taking -into account the number of probes per gene on the array, as well as taking -into account multi-gene associated probes.") - (license license:gpl2))) - (define-public r-msdata (package (name "r-msdata") @@ -4220,6 +4125,51 @@ scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.") (license license:gpl3))) +(define-public r-cellid + (package + (name "r-cellid") + (version "1.8.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "CelliD" version)) + (sha256 + (base32 + "0vigvqjrlqbi5kviaj8qvyq3v8afgbc5pjrz7zmx2ckf4hdp0g03")))) + (properties `((upstream-name . "CelliD"))) + (build-system r-build-system) + (propagated-inputs + (list r-data-table + r-biocparallel + r-fastmatch + r-fgsea + r-ggplot2 + r-glue + r-irlba + r-matrix + r-matrixstats + r-pbapply + r-rcpp + r-rcpparmadillo + r-reticulate + r-rtsne + r-seurat + r-stringr + r-tictoc + r-singlecellexperiment + r-summarizedexperiment + r-umap)) + (native-inputs (list r-knitr r-scater)) + (home-page "https://bioconductor.org/packages/CelliD") + (synopsis + "Single cell gene signature extraction using multiple correspondence analysis") + (description + "CelliD is a clustering-free method for extracting per-cell gene +signatures from scRNA-seq. CelliD allows unbiased cell identity recognition +across different donors, tissues-of-origin, model organisms and single-cell +omics protocols. The package can also be used to explore functional pathways +enrichment in single cell data.") + (license license:gpl3))) + (define-public r-coverageview (package (name "r-coverageview") @@ -5008,6 +4958,25 @@ Beta-Binomial distributions.") ;; Any version of the GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-dyndoc + (package + (name "r-dyndoc") + (version "1.78.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "DynDoc" version)) + (sha256 + (base32 + "16cb4pby6ja0xy8ygbgr6zfbyp4agyhlds5sayc5ryq50vafykah")))) + (properties `((upstream-name . "DynDoc"))) + (build-system r-build-system) + (home-page "https://bioconductor.org/packages/DynDoc") + (synopsis "Dynamic document tools") + (description + "This package provides a set of functions to create and interact with +dynamic documents and vignettes.") + (license license:artistic2.0))) + (define-public r-bluster (package (name "r-bluster") @@ -5366,6 +5335,37 @@ pre-calculated probe set quality scores that were used to define the mapping.") (license license:artistic2.0))) +(define-public r-nebulosa + (package + (name "r-nebulosa") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Nebulosa" version)) + (sha256 + (base32 + "0lqm9mfmaxdhhs9di2kjg2rixng78lrrikyp7blmpyqk4c41j3nh")))) + (properties `((upstream-name . "Nebulosa"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 + r-ks + r-matrix + r-patchwork + r-seurat + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/powellgenomicslab/Nebulosa") + (synopsis + "Single-cell data visualisation using kernel gene-weighted density estimation") + (description + "This package provides a enhanced visualization of single-cell data based +on gene-weighted density estimation. Nebulosa recovers the signal from +dropped-out features and allows the inspection of the joint expression from +multiple features (e.g. genes). @code{Seurat} and @code{SingleCellExperiment} +objects can be used within Nebulosa.") + (license license:gpl3))) + ;; This is a CRAN package, but it depends on Bioconductor packages. (define-public r-nmf (package @@ -5442,14 +5442,14 @@ analysis.") (define-public r-affycomp (package (name "r-affycomp") - (version "1.76.0") + (version "1.76.1") (source (origin (method url-fetch) (uri (bioconductor-uri "affycomp" version)) (sha256 (base32 - "1bsav6d3dhn2fs7gjd1jvrb448ckxw5l6ikrdv63cdnnjk0dxl62")))) + "0wccj8q8sl0zc68nr5qf1qih8awqf1h6bwi5hq9d7r59p4g4r9n1")))) (properties `((upstream-name . "affycomp"))) (build-system r-build-system) (propagated-inputs (list r-biobase)) @@ -6677,6 +6677,34 @@ other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.") (license license:gpl2+))) +(define-public r-enhancedvolcano + (package + (name "r-enhancedvolcano") + (version "1.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "EnhancedVolcano" version)) + (sha256 + (base32 + "1mcyhgdvfmkkh0rlhf51an7j1zi96lqdhifki2aqmlx0lqvg4qxq")))) + (properties `((upstream-name . "EnhancedVolcano"))) + (build-system r-build-system) + (propagated-inputs (list r-ggplot2 r-ggrepel)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/kevinblighe/EnhancedVolcano") + (synopsis + "Publication-ready volcano plots with enhanced coloring and labeling") + (description + "Volcano plots represent a useful way to visualise the results of +differential expression analyses. This package provides a highly-configurable +function that produces publication-ready volcano plots. EnhancedVolcano will +attempt to fit as many point labels in the plot window as possible, thus +avoiding clogging up the plot with labels that could not otherwise have been +read. Other functionality allows the user to identify up to 4 different types +of attributes in the same plot space via color, shape, size, and shade +parameter configurations.") + (license license:gpl3))) + (define-public r-enmix (package (name "r-enmix") @@ -6968,6 +6996,37 @@ junction detection, and working with the nucleotide content of the alignments.") (license license:artistic2.0))) +(define-public r-genomicdatacommons + (package + (name "r-genomicdatacommons") + (version "1.24.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GenomicDataCommons" version)) + (sha256 + (base32 + "0dgvhi6nbc1qvrdwww2r39gxd2xmbadvy03lxh5nny9pyhhdlz3l")))) + (properties `((upstream-name . "GenomicDataCommons"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-genomicranges + r-httr + r-iranges + r-jsonlite + r-magrittr + r-rappdirs + r-readr + r-rlang + r-tibble + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/GenomicDataCommons") + (synopsis "NIH/NCI genomic data commons access") + (description + "This package lets you programmatically access the NIH/NCI Genomic Data +Commons RESTful service.") + (license license:artistic2.0))) + (define-public r-genomicfeatures (package (name "r-genomicfeatures") @@ -7098,6 +7157,38 @@ profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.") (license license:gpl2))) +(define-public r-globalancova + (package + (name "r-globalancova") + (version "4.18.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GlobalAncova" version)) + (sha256 + (base32 + "1fld18rmi6rqm2nr549a4740w1iq3mf5df67v9ba6h42r4abs1ar")))) + (properties `((upstream-name . "GlobalAncova"))) + (build-system r-build-system) + (propagated-inputs (list r-annotate + r-annotationdbi + r-biobase + r-corpcor + r-dendextend + r-globaltest + r-gseabase + r-vgam)) + (home-page "https://bioconductor.org/packages/GlobalAncova") + (synopsis "Global test for groups of variables via model comparisons") + (description + "This package supports the computation of an F-test for the association +between expression values and clinical entities. In many cases a two way +layout with gene and a dichotomous group as factors will be considered. +However, adjustment for other covariates and the analysis of arbitrary +clinical variables, interactions, gene co-expression, time series data and so +on is also possible. The test is carried out by comparison of corresponding +linear models via the extra sum of squares principle.") + (license license:gpl2+))) + (define-public r-globaltest (package (name "r-globaltest") @@ -7183,6 +7274,46 @@ testing and other simple calculations.") Enrichment Analysis} (GSEA).") (license license:artistic2.0))) +(define-public r-gsva + (package + (name "r-gsva") + (version "1.48.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GSVA" version)) + (sha256 + (base32 + "1y0dz9ayyrz4ylppa8f4m4b20yajzdl1sz4wpz8kcsfhh71ii64y")))) + (properties `((upstream-name . "GSVA"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase + r-biocparallel + r-biocsingular + r-delayedarray + r-delayedmatrixstats + r-gseabase + r-hdf5array + r-iranges + r-matrix + r-s4vectors + r-singlecellexperiment + r-sparsematrixstats + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/rcastelo/GSVA") + (synopsis "Gene Set Variation Analysis for microarray and RNA-seq data") + (description + "Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised +method for estimating variation of gene set enrichment through the samples of +a expression data set. GSVA performs a change in coordinate systems, +transforming the data from a gene by sample matrix to a gene-set by sample +matrix, thereby allowing the evaluation of pathway enrichment for each sample. +This new matrix of GSVA enrichment scores facilitates applying standard +analytical methods like functional enrichment, survival analysis, clustering, +CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric +manner.") + (license license:gpl2+))) + (define-public r-harshlight (package (name "r-harshlight") @@ -7245,6 +7376,39 @@ matrix to solve the memory problem.") the Human Protein Atlas project.") (license license:artistic2.0))) +(define-public r-raggedexperiment + (package + (name "r-raggedexperiment") + (version "1.24.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RaggedExperiment" version)) + (sha256 + (base32 + "1xs7dz5mkh9zs078g2a0izij8vxrwhzh7gyjglp057gicsca0hal")))) + (properties `((upstream-name . "RaggedExperiment"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-genomeinfodb + r-genomicranges + r-iranges + r-matrix + r-matrixgenerics + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/RaggedExperiment") + (synopsis "Representation of sparse experiments and assays across samples") + (description + "This package provides a flexible representation of copy number, +mutation, and other data that fit into the ragged array schema for genomic +location data. The basic representation of such data provides a rectangular +flat table interface to the user with range information in the rows and +samples/specimen in the columns. The @code{RaggedExperiment} class derives +from a @code{GRangesList} representation and provides a semblance of a +rectangular dataset.") + (license license:artistic2.0))) + (define-public r-rhtslib (package (name "r-rhtslib") @@ -7659,6 +7823,26 @@ resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq.") (license license:artistic2.0))) +(define-public r-mfuzz + (package + (name "r-mfuzz") + (version "2.60.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Mfuzz" version)) + (sha256 + (base32 + "0rfna5ycwkx4xb2gv1wpfn7f7nz6f79w5nlkb7719l5730d81wnz")))) + (properties `((upstream-name . "Mfuzz"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-e1071 r-tkwidgets)) + (home-page "http://mfuzz.sysbiolab.eu/") + (synopsis "Soft clustering of time series gene expression data") + (description + "This is a package for noise-robust soft clustering of gene expression +time-series data (including a graphical user interface).") + (license license:gpl2))) + (define-public r-mmuphin (package (name "r-mmuphin") @@ -8725,6 +8909,46 @@ tab-delimited (tabix) files.") "This package models a RESTful service as if it were a nested R list.") (license license:artistic2.0))) +(define-public r-rtcgatoolbox + (package + (name "r-rtcgatoolbox") + (version "2.30.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "RTCGAToolbox" version)) + (sha256 + (base32 + "03p5rgjzc1265q60jkvk92vhcib5wdnv6bz997r70q9c39y03wm5")))) + (properties `((upstream-name . "RTCGAToolbox"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-data-table + r-delayedarray + r-genomeinfodb + r-genomicranges + r-httr + r-raggedexperiment + r-rcircos + r-rcurl + r-rjsonio + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment + r-tcgautils)) + (native-inputs (list r-knitr)) + (home-page "http://mksamur.github.io/RTCGAToolbox/") + (synopsis "Export TCGA Firehose data") + (description + "Managing data from large scale projects such as The Cancer Genome +Atlas (TCGA) for further analysis is an important and time consuming step for +research projects. Several efforts, such as Firehose project, make TCGA +pre-processed data publicly available via web services and data portals but it +requires managing, downloading and preparing the data for following steps. +This package provides an extensible R based data client for Firehose +pre-processed data.") + (license license:gpl2))) + (define-public r-rtracklayer (package (name "r-rtracklayer") @@ -9030,6 +9254,36 @@ facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.") (license license:artistic2.0))) +(define-public r-seqarray + (package + (name "r-seqarray") + (version "1.40.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SeqArray" version)) + (sha256 + (base32 + "1771vk23psjavvi1nf2z8i2xawygdh4amawlijnskci8y9w4x5dm")))) + (properties `((upstream-name . "SeqArray"))) + (build-system r-build-system) + (propagated-inputs (list r-biostrings + r-gdsfmt + r-genomeinfodb + r-genomicranges + r-iranges + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zhengxwen/SeqArray") + (synopsis + "Data management of large-scale whole-genome sequence variant calls") + (description + "This package supports data management of large-scale whole-genome +sequencing variant calls with thousands of individuals: genotypic data (e.g., +SNVs, indels and structural variation calls) and annotations in SeqArray GDS +files are stored in an array-oriented and compressed manner, with efficient +data access using the R programming language.") + (license license:gpl3))) + (define-public r-seqlogo (package (name "r-seqlogo") @@ -9188,6 +9442,101 @@ this package. It also provides functionalities for visualizing, summarizing and comparing the clusterings.") (license license:expat))) +(define-public r-singscore + (package + (name "r-singscore") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "singscore" version)) + (sha256 + (base32 + "1s1kyvkbfgwskf0hi4b44c2yx256rjp1yk9ijpld9qlm7z7pi67q")))) + (properties `((upstream-name . "singscore"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase + r-biocparallel + r-edger + r-ggplot2 + r-ggrepel + r-gseabase + r-magrittr + r-matrixstats + r-plotly + r-plyr + r-rcolorbrewer + r-reshape + r-reshape2 + r-s4vectors + r-summarizedexperiment + r-tidyr)) + (native-inputs (list r-knitr)) + (home-page "https://davislaboratory.github.io/singscore/") + (synopsis "Rank-based single-sample gene set scoring method") + (description + "This package provides a simple single-sample gene signature scoring +method that uses rank-based statistics to analyze the sample's gene expression +profile. It scores the expression activities of gene sets at a single-sample +level.") + (license license:gpl3))) + +(define-public r-tcgautils + (package + (name "r-tcgautils") + (version "1.20.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "TCGAutils" version)) + (sha256 + (base32 + "0nnfrd5x3mii9adizvz79jinlxn2lhg4civ9v0wwygmdhk7rrm1n")))) + (properties `((upstream-name . "TCGAutils"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-biocgenerics + r-genomeinfodb + r-genomicdatacommons + r-genomicfeatures + r-genomicranges + r-iranges + r-multiassayexperiment + r-raggedexperiment + r-rvest + r-s4vectors + r-stringr + r-summarizedexperiment + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/TCGAutils") + (synopsis "TCGA utility functions for data management") + (description + "This package provides a suite of helper functions for checking and +manipulating TCGA data including data obtained from the @code{curatedTCGAData} +experiment package. These functions aim to simplify and make working with +TCGA data more manageable. Exported functions include those that import data +from flat files into Bioconductor objects, convert row annotations, and +identifier translation via the GDC API.") + (license license:artistic2.0))) + +(define-public r-tkwidgets + (package + (name "r-tkwidgets") + (version "1.78.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tkWidgets" version)) + (sha256 + (base32 + "1xp0gdfrhhfzfww4ig3y90f7334y24rhzrmlxmm4wav8slvcran2")))) + (properties `((upstream-name . "tkWidgets"))) + (build-system r-build-system) + (propagated-inputs (list r-dyndoc r-widgettools)) + (home-page "https://bioconductor.org/packages/tkWidgets") + (synopsis "R based tk widgets") + (description + "This package implements widgets to provide user interfaces.") + (license license:artistic2.0))) + (define-public r-transcriptr (package (name "r-transcriptr") @@ -9365,6 +9714,37 @@ into features. These features can be processed with any number of statistical tools either included in speaq or available elsewhere on CRAN.") (license license:asl2.0))) +(define-public r-spectra + (package + (name "r-spectra") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "Spectra" version)) + (sha256 + (base32 + "0vq5ha5m1vny7nrhgfmmkjd30zv0xaignp1a1m0xj08lnhkkmd69")))) + (properties `((upstream-name . "Spectra"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-biocparallel + r-fs + r-iranges + r-mscoreutils + r-protgenerics + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/Spectra") + (synopsis "Spectra infrastructure for mass spectrometry data") + (description + "The Spectra package defines an efficient infrastructure for storing and +handling mass spectrometry spectra and functionality to subset, process, +visualize and compare spectra data. It provides different +implementations (backends) to store mass spectrometry data. These comprise +backends tuned for fast data access and processing and backends for very large +data sets ensuring a small memory footprint.") + (license license:artistic2.0))) + (define-public r-stager (package (name "r-stager") @@ -9493,6 +9873,33 @@ typically represent genomic ranges of interest and the columns represent samples.") (license license:artistic2.0))) +(define-public r-survcomp + (package + (name "r-survcomp") + (version "1.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "survcomp" version)) + (sha256 + (base32 + "1va0ijx3qk3rjhzaflygfwlzn5a670y833qly8in8p5r3al9bdj6")))) + (properties `((upstream-name . "survcomp"))) + (build-system r-build-system) + (propagated-inputs (list r-bootstrap + r-ipred + r-kernsmooth + r-prodlim + r-rmeta + r-suppdists + r-survival + r-survivalroc)) + (home-page "https://www.pmgenomics.ca/bhklab/") + (synopsis "Performance assessment and comparison for survival analysis") + (description + "This is a package for the assessment and comparison of the performance +of risk prediction (survival) models.") + (license license:artistic2.0))) + (define-public r-sva (package (name "r-sva") @@ -10009,6 +10416,41 @@ arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).") (license license:lgpl2.0+))) +(define-public r-qfeatures + (package + (name "r-qfeatures") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "QFeatures" version)) + (sha256 + (base32 + "1xnmd14nf4cqbfxkjsl6af312k7l27ars5g8qdnljylkn8kq276z")))) + (properties `((upstream-name . "QFeatures"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationfilter + r-biobase + r-biocgenerics + r-igraph + r-iranges + r-lazyeval + r-mscoreutils + r-multiassayexperiment + r-plotly + r-protgenerics + r-s4vectors + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/RforMassSpectrometry/QFeatures") + (synopsis "Quantitative features for mass spectrometry data") + (description + "The QFeatures infrastructure enables the management and processing of +quantitative features for high-throughput mass spectrometry assays. It +provides a familiar Bioconductor user experience to manages quantitative data +across different assay levels (such as peptide spectrum matches, peptides and +proteins) in a coherent and tractable format.") + (license license:artistic2.0))) + (define-public r-quantsmooth (package (name "r-quantsmooth") @@ -10414,6 +10856,36 @@ expressed genes in DNA microarray experiments.") fitting of some classes of graphical Markov models.") (license license:gpl2+))) +(define-public r-ggtreeextra + (package + (name "r-ggtreeextra") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "ggtreeExtra" version)) + (sha256 + (base32 + "19xikly6ksh03kgpz35wj2d2gdbpikhrk71ahj9ghhkmlwdyjbcr")))) + (properties `((upstream-name . "ggtreeExtra"))) + (build-system r-build-system) + (propagated-inputs (list r-cli + r-ggnewscale + r-ggplot2 + r-ggtree + r-magrittr + r-rlang + r-tidytree)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/YuLab-SMU/ggtreeExtra/") + (synopsis + "Add geometric layers On circular or other layout tree of ggtree") + (description + "ggtreeExtra extends the method for mapping and visualizing associated +data on phylogenetic tree using ggtree. These associated data can be +presented on the external panels to circular layout, fan layout, or other +rectangular layout tree built by ggtree with the grammar of ggplot2.") + (license license:gpl3+))) + ;; This is a CRAN package, but it depends on a bunch of Bioconductor packages. (define-public r-ggpicrust2 (package @@ -11126,6 +11598,40 @@ PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.") (license license:gpl2))) +(define-public r-plyranges + (package + (name "r-plyranges") + (version "1.20.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "plyranges" version)) + (sha256 + (base32 + "1qv8snpcxpg16v5ji7sq3bnmgrgghz9h4mh246mcnnxfhi44b6nv")))) + (properties `((upstream-name . "plyranges"))) + (build-system r-build-system) + (propagated-inputs (list r-biocgenerics + r-dplyr + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-iranges + r-magrittr + r-rlang + r-rsamtools + r-rtracklayer + r-s4vectors + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/plyranges") + (synopsis "Fluent interface for manipulating GenomicRanges") + (description + "This package provides a dplyr-like interface for interacting with the +common Bioconductor classes @code{Ranges} and @code{GenomicRanges}. By +providing a grammatical and consistent way of manipulating these classes their +accessiblity for new Bioconductor users is hopefully increased.") + (license license:artistic2.0))) + (define-public r-inspect (package (name "r-inspect") @@ -11281,14 +11787,14 @@ multiplication.") (define-public r-treeio (package (name "r-treeio") - (version "1.24.1") + (version "1.24.2") (source (origin (method url-fetch) (uri (bioconductor-uri "treeio" version)) (sha256 (base32 - "1jwjnwakinfqfx8ajbl58lqdhsq06a25phxy3vsprh1glj37smf7")))) + "0xjhyrqpr54aaj4han69ndkbmz5kwnf01adh80v2r8jc8jwdfy6m")))) (properties `((upstream-name . "treeio"))) (build-system r-build-system) (propagated-inputs @@ -11800,14 +12306,14 @@ independent of the p-value under the null hypothesis.") (define-public r-icobra (package (name "r-icobra") - (version "1.28.0") + (version "1.28.1") (source (origin (method url-fetch) (uri (bioconductor-uri "iCOBRA" version)) (sha256 (base32 - "1dirwfmjl15lqh1dx1yhaqbfiz5iwzp03d3g64iy31nzi8sha4qq")))) + "120bcakhhl6xqsfclzgmn7rcxmld289bjl6j7nrli7aiq5ilz8h4")))) (properties `((upstream-name . "iCOBRA"))) (build-system r-build-system) (propagated-inputs @@ -12588,6 +13094,56 @@ model.") methylation arrays.") (license license:artistic2.0))) +(define-public r-missmethyl + (package + (name "r-missmethyl") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "missMethyl" version)) + (sha256 + (base32 + "1jvrdr57mv93pcbyazcg1bcx1zd0kp72hi1if839gw54hk3igs3h")))) + (properties `((upstream-name . "missMethyl"))) + (build-system r-build-system) + (propagated-inputs + (list r-annotationdbi + r-biasedurn + r-biobase + r-biocgenerics + r-genomicranges + r-go-db + r-illuminahumanmethylation450kanno-ilmn12-hg19 + r-illuminahumanmethylation450kmanifest + r-illuminahumanmethylationepicanno-ilm10b4-hg19 + r-illuminahumanmethylationepicmanifest + r-iranges + r-limma + r-methylumi + r-minfi + r-org-hs-eg-db + r-ruv + r-s4vectors + r-statmod + r-stringr + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/missMethyl") + (synopsis "Analyzing Illumina HumanMethylation BeadChip data") + (description + "This is a package for normalization, testing for differential +variability and differential methylation and gene set testing for data from +Illumina's Infinium HumanMethylation arrays. The normalization procedure is +subset-quantile within-array normalization (SWAN), which allows Infinium I and +II type probes on a single array to be normalized together. The test for +differential variability is based on an empirical Bayes version of Levene's +test. Differential methylation testing is performed using RUV, which can +adjust for systematic errors of unknown origin in high-dimensional data by +using negative control probes. Gene ontology analysis is performed by taking +into account the number of probes per gene on the array, as well as taking +into account multi-gene associated probes.") + (license license:gpl2))) + (define-public r-methylumi (package (name "r-methylumi") @@ -12991,14 +13547,14 @@ information about samples and features can be added to the plot.") (define-public r-gosemsim (package (name "r-gosemsim") - (version "2.26.0") + (version "2.26.1") (source (origin (method url-fetch) (uri (bioconductor-uri "GOSemSim" version)) (sha256 (base32 - "1pg86z4vbrp59kpq7zpscnjw9cgfkdqjrdp9zjvdf3xghgjvwl9a")))) + "15z7wqnp0s8fiysl3qc76pjaj3xik2br2mz2z3nmf28vxig69mx9")))) (properties `((upstream-name . "GOSemSim"))) (build-system r-build-system) (propagated-inputs @@ -13211,14 +13767,14 @@ All the visualization methods are developed based on ggplot2 graphics.") (define-public r-clusterprofiler (package (name "r-clusterprofiler") - (version "4.8.1") + (version "4.8.2") (source (origin (method url-fetch) (uri (bioconductor-uri "clusterProfiler" version)) (sha256 (base32 - "1vcqzk5a2y3g2vv5vlpvcpd45xdq6rs5djnrdkww536cwkas9zvy")))) + "0iijby2j9i6sbdc3iwhqqb8xlz25k3dpiyq91p7yybggpr2p1nw4")))) (properties `((upstream-name . "clusterProfiler"))) (build-system r-build-system) @@ -15511,14 +16067,14 @@ interact with gated cytometry data.") (define-public r-flowcore (package (name "r-flowcore") - (version "2.12.0") + (version "2.12.1") (source (origin (method url-fetch) (uri (bioconductor-uri "flowCore" version)) (sha256 (base32 - "1zkv4nwc6vg0jd4rh8mswdhr9cbq7ll98424hl5vs9hklal6kw8d")))) + "09jirhhf1qfanyhbq1ybmw6smv8163b7cqgj0qw69grvs8bb0b6m")))) (properties `((upstream-name . "flowCore"))) (build-system r-build-system) (propagated-inputs @@ -16841,6 +17397,37 @@ non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).") (license license:artistic2.0))) +(define-public r-ucell + (package + (name "r-ucell") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "UCell" version)) + (sha256 + (base32 + "01qcwmiqri4xvwr3j4k1g062rfj6bbc0bvh0ifq1jq2xrm1azw9y")))) + (properties `((upstream-name . "UCell"))) + (build-system r-build-system) + (propagated-inputs (list r-biocneighbors + r-biocparallel + r-data-table + r-matrix + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/carmonalab/UCell") + (synopsis "Rank-based signature enrichment analysis for single-cell data") + (description + "UCell is a package for evaluating gene signatures in single-cell datasets. +UCell signature scores, based on the Mann-Whitney U statistic, are robust to +dataset size and heterogeneity, and their calculation demands less computing +time and memory than other available methods, enabling the processing of large +datasets in a few minutes even on machines with limited computing power. +UCell can be applied to any single-cell data matrix, and includes functions to +directly interact with SingleCellExperiment and Seurat objects.") + (license license:gpl3))) + (define-public r-unifiedwmwqpcr (package (name "r-unifiedwmwqpcr") @@ -17777,14 +18364,14 @@ also known as views, in a controlled vocabulary.") (define-public r-experimenthub (package (name "r-experimenthub") - (version "2.8.0") + (version "2.8.1") (source (origin (method url-fetch) (uri (bioconductor-uri "ExperimentHub" version)) (sha256 (base32 - "0n55p4n2aadxh182lxxms3bk4bpajamivvqj06v09q2n9xnhjs7k")))) + "1md6lan98h95jv776zyvl5im39gz4h6fdxw571vfahgr4b2nxvm4")))) (properties `((upstream-name . "ExperimentHub"))) (build-system r-build-system) (propagated-inputs @@ -18782,6 +19369,39 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +(define-public r-beadarray + (package + (name "r-beadarray") + (version "2.50.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "beadarray" version)) + (sha256 + (base32 + "0rd41193rq6v4a97ibp0l2bz140nsv91plhn7iim8d8n9hgxqhjp")))) + (properties `((upstream-name . "beadarray"))) + (build-system r-build-system) + (propagated-inputs (list r-annotationdbi + r-beaddatapackr + r-biobase + r-biocgenerics + r-genomicranges + r-ggplot2 + r-hexbin + r-illuminaio + r-iranges + r-limma + r-reshape2)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/beadarray") + (synopsis + "Quality assessment and low-level analysis for Illumina BeadArray data") + (description + "The package is able to read bead-level data (raw TIFFs and text files) +output by BeadScan as well as bead-summary data from BeadStudio. Methods for +quality assessment and low-level analysis are provided.") + (license license:expat))) + (define-public r-beadarraysnp (package (name "r-beadarraysnp") @@ -18802,6 +19422,26 @@ matrices.") performs copy number calculations and reports.") (license license:gpl2))) +(define-public r-beaddatapackr + (package + (name "r-beaddatapackr") + (version "1.52.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "BeadDataPackR" version)) + (sha256 + (base32 + "0hm4brxg2rxazdcnhjiz6f4di2q8wssrrp35m79vm93sac9w42y3")))) + (properties `((upstream-name . "BeadDataPackR"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/BeadDataPackR") + (synopsis "Compression of Illumina BeadArray data") + (description + "This package provides functionality for the compression and +decompression of raw bead-level data from the Illumina BeadArray platform.") + (license license:gpl2))) + ;; This package includes files that have been taken from kentutils. Some ;; parts of kentutils are not released under a free license, but this package ;; only uses files that are also found in the free parts of kentutils. @@ -19217,6 +19857,38 @@ operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.") (license license:expat))) +(define-public r-spatialexperiment + (package + (name "r-spatialexperiment") + (version "1.10.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SpatialExperiment" version)) + (sha256 + (base32 + "18fcfyjvp9nzadlicsnz62wva8ik0z6jqg1b906avm2vk6rbxw70")))) + (properties `((upstream-name . "SpatialExperiment"))) + (build-system r-build-system) + (propagated-inputs (list r-biocfilecache + r-biocgenerics + r-dropletutils + r-magick + r-rjson + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/drighelli/SpatialExperiment") + (synopsis "S4 class for spatially resolved -omics data") + (description + "This package defines an S4 class for storing data from spatial -omics +experiments. The class extends SingleCellExperiment to support storage and +retrieval of additional information from spot-based and molecule-based +platforms, including spatial coordinates, images, and image metadata. A +specialized constructor function is included for data from the 10x Genomics +Visium platform.") + (license license:gpl3))) + (define-public r-delayedmatrixstats (package (name "r-delayedmatrixstats") @@ -19751,6 +20423,37 @@ with your data.") EMBL-EBI GWAS catalog.") (license license:artistic2.0))) +(define-public r-gwastools + (package + (name "r-gwastools") + (version "1.46.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GWASTools" version)) + (sha256 + (base32 + "1g86xg2d9wi6xijhc89zxhbw190aviw9nkwvbwgz85jf71wf34hv")))) + (properties `((upstream-name . "GWASTools"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase + r-data-table + r-dbi + r-dnacopy + r-gdsfmt + r-gwasexacthw + r-lmtest + r-logistf + r-quantsmooth + r-rsqlite + r-sandwich + r-survival)) + (home-page "https://github.com/smgogarten/GWASTools") + (synopsis "Tools for Genome Wide Association Studies") + (description + "This package provides classes for storing very large GWAS data sets and +annotation, and functions for GWAS data cleaning and analysis.") + (license license:artistic2.0))) + (define-public r-kegggraph (package (name "r-kegggraph") @@ -19957,6 +20660,41 @@ segmented data for individual and multiple arrays.") ;; Expanded from GPL (license (list license:gpl2+ license:gpl3+)))) +(define-public r-snprelate + (package + (name "r-snprelate") + (version "1.34.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "SNPRelate" version)) + (sha256 + (base32 + "0js932qvhlwmnrr2jfvsch2zm6w6a1z5wydns3r1bw24r817dlgh")))) + (properties `((upstream-name . "SNPRelate"))) + (build-system r-build-system) + (propagated-inputs (list r-gdsfmt)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/zhengxwen/SNPRelate") + (synopsis + "Toolset for relatedness and Principal Component Analysis of SNP data") + (description + "Genome-wide association studies (GWAS) are widely used to investigate +the genetic basis of diseases and traits, but they pose many computational +challenges. The R package SNPRelate provides a binary format for +single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic +Data Structure (GDS) data files. The GDS format offers the efficient +operations specifically designed for integers with two bits, since a SNP could +occupy only two bits. SNPRelate is also designed to accelerate two key +computations on SNP data using parallel computing for multi-core symmetric +multiprocessing computer architectures: Principal Component Analysis (PCA) and +relatedness analysis using Identity-By-Descent measures. The SNP GDS format +is also used by the GWASTools package with the support of S4 classes and +generic functions. The extended GDS format is implemented in the SeqArray +package to support the storage of single nucleotide variations (SNVs), +insertion/deletion polymorphism (indel) and structural variation calls in +whole-genome and whole-exome variant data.") + (license license:gpl3))) + (define-public r-snpstats (package (name "r-snpstats") |