diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 662 |
1 files changed, 660 insertions, 2 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index c2fa26cb59..d2eb9a0daf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5,13 +5,14 @@ ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> ;;; 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 © 2019, 2020, 2021, 2022, 2023 Simon Tournier <zimon.toutoune@gmail.com> ;;; Copyright © 2020 Peter Lo <peterloleungyau@gmail.com> -;;; Copyright © 2020, 2021, 2022 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2020-2023 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2020 Jakub Kądziołka <kuba@kadziolka.net> ;;; Copyright © 2021 Hong Li <hli@mdc-berlin.de> ;;; Copyright © 2021 Tim Howes <timhowes@lavabit.com> ;;; Copyright © 2021 Nicolas Vallet <nls.vallet@gmail.com> +;;; Copyright © 2023 Navid Afkhami <Navid.Afkhami@mdc-berlin.de> ;;; ;;; This file is part of GNU Guix. ;;; @@ -114,6 +115,33 @@ analysis.") based on mapping using Entrez Gene identifiers.") (license license:artistic2.0))) +(define-public r-pd-mapping50k-xba240 + (package + (name "r-pd-mapping50k-xba240") + (version "3.12.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "pd.mapping50k.xba240" version + 'annotation)) + (sha256 + (base32 "1a1f3lh5ywhyjawdbj2fzban85c8jz70lfcv3pagd5piincjwxq8")))) + (properties `((upstream-name . "pd.mapping50k.xba240"))) + (build-system r-build-system) + (propagated-inputs + (list r-biostrings + r-dbi + r-iranges + r-oligo + r-oligoclasses + r-rsqlite + r-s4vectors)) + (home-page "https://bioconductor.org/packages/pd.mapping50k.xba240") + (synopsis "Platform design info for Affymetrix Mapping50K_Xba240") + (description "This package provides platform design info for Affymetrix +Mapping50K_Xba240 (pd.mapping50k.xba240).") + (license license:artistic2.0))) + (define-public r-reactome-db (package (name "r-reactome-db") @@ -1247,6 +1275,29 @@ demonstration purposes in the @code{AneuFinder} package.") from Illumina 450k methylation arrays.") (license license:artistic2.0))) +(define-public r-bcellviper + (package + (name "r-bcellviper") + (version "1.34.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "bcellViper" version + 'experiment)) + (sha256 + (base32 + "1fpgh70x2r68v0ximgcdphnyzq2hgiwbamyhbac3yka8flhrd1fm")))) + (properties `((upstream-name . "bcellViper"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase)) + (home-page "https://bioconductor.org/packages/bcellViper") + (synopsis + "Transcriptional interactome and normal human B-cell expression data") + (description + "This is a tool for human B-cell context-specific transcriptional +regulatory network. In addition, this package provides a human normal B-cells +dataset for the examples in package viper.") + (license license:gpl2+))) + (define-public r-bladderbatch (package (name "r-bladderbatch") @@ -1291,6 +1342,26 @@ from Illumina 450k methylation arrays.") biscuiteer.") (license license:gpl3))) +(define-public r-breakpointrdata + (package + (name "r-breakpointrdata") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointRdata" version 'experiment)) + (sha256 + (base32 + "0f23i4ynb4vgn22c3d2l64z92rzv3qnwd4j8qyvalklrxkwilhfn")))) + (properties `((upstream-name . "breakpointRdata"))) + (build-system r-build-system) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/breakpointRdata") + (synopsis "Strand-seq data for demonstration purposes") + (description + "This package is a collection of Strand-seq data. The main purpose is to +demonstrate functionalities of the @code{breakpointR} package.") + (license license:expat))) + (define-public r-celldex (package (name "r-celldex") @@ -1410,6 +1481,25 @@ genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.") (license license:gpl3+))) +(define-public r-italicsdata + (package + (name "r-italicsdata") + (version "2.36.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICSData" version 'experiment)) + (sha256 + (base32 "09d2igic3b5p7wpq98hb2lffxm1nfq9mwmnqlbdn3jv49pgz3hmw")))) + (properties `((upstream-name . "ITALICSData"))) + (build-system r-build-system) + (home-page "http://bioinfo.curie.fr") + (synopsis "ITALICS data") + (description "This package provides data needed to use the ITALICS +package.") + ;; Expanded from GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-macrophage (package (name "r-macrophage") @@ -1736,6 +1826,48 @@ expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.") (license license:gpl3+))) +(define-public r-adacgh2 + (package + (name "r-adacgh2") + (version "2.38.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ADaCGH2" version)) + (sha256 + (base32 "0g9x3lnr56035wq9ijdcri4sz5pwj8184yxm415gmsxrii9xvpfd")))) + (properties `((upstream-name . "ADaCGH2"))) + (build-system r-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'python3-compatibility + (lambda _ + (substitute* "inst/imagemap-example/toMap.py" + (("print nameMap") "print(nameMap)"))))))) + (inputs (list python-wrapper)) + (propagated-inputs + (list r-acgh + r-bit + r-cluster + r-dnacopy + r-ff + r-glad + r-snapcgh + r-tilingarray + r-waveslim)) + (home-page "https://github.com/rdiaz02/adacgh2") + (synopsis "Big data analysis from aCGH experiments") + (description + "This package analyzes and creates plots of array @acronym{CGH, +comparative genomic hybridization} data. Also, it allows usage of +@acronym{CBS, Circular Binary Segementation}, wavelet-based smoothing, HMM, +BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking +or with clusters, including MPI and sockets clusters) and use @code{ff} for +storing data.") + (license license:gpl3+))) + (define-public r-adam (package (name "r-adam") @@ -2443,6 +2575,47 @@ Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.") (license license:artistic2.0))) +(define-public r-anvil + (package + (name "r-anvil") + (version "1.10.1") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AnVIL" version)) + (sha256 + (base32 + "0iqsffkrxv28g9cddx2w05f2dbscwxhh6bpizwa8xaxhvn5bcpsv")))) + (properties `((upstream-name . "AnVIL"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocmanager + r-dplyr + r-dt + r-futile-logger + r-htmltools + r-httr + r-jsonlite + r-miniui + r-rapiclient + r-rlang + r-shiny + r-tibble + r-tidyr + r-tidyselect)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/AnVIL") + (synopsis "Provides access to AnVIL, Terra, Leonardo and other projects") + (description + "The AnVIL is a cloud computing resource developed in part by the +National Human Genome Research Institute. The AnVIL package provides end-user +and developer functionality. AnVIL provides fast binary package installation, +utilities for working with Terra/AnVIL table and data resources, and +convenient functions for file movement to and from Google cloud storage. For +developers, AnVIL provides programatic access to the Terra, Leonardo, Rawls, +Dockstore, and Gen3 RESTful programming interface, including helper functions +to transform JSON responses to formats more amenable to manipulation in R.") + (license license:artistic2.0))) + (define-public r-aldex2 (package (name "r-aldex2") @@ -2598,6 +2771,59 @@ mapped reads). It is currently designed for un-stranded paired-end RNA-seq data.") (license license:gpl2+))) +(define-public r-alpsnmr + (package + (name "r-alpsnmr") + (version "4.0.2") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "AlpsNMR" version)) + (sha256 + (base32 + "1y4qqc6l8flv5ns4qwzjwmcykm6zcm4jg097mn8xyp7mnxymy7pl")))) + (properties `((upstream-name . "AlpsNMR"))) + (build-system r-build-system) + (propagated-inputs + (list r-baseline + r-biocparallel + r-dplyr + r-fs + r-future + r-generics + r-ggplot2 + r-glue + r-htmltools + r-magrittr + r-matrixstats + r-mixomics + r-pcapp + r-purrr + r-readxl + r-reshape2 + r-rlang + r-rmarkdown + r-scales + r-signal + r-speaq + r-stringr + r-tibble + r-tidyr + r-tidyselect + r-vctrs)) + (native-inputs (list r-knitr)) + (home-page "https://sipss.github.io/AlpsNMR/") + (synopsis "Automated spectral processing system for NMR") + (description + "This package reads Bruker @acronym{NMR, Nuclear Magnetic Resonance} data +directories both zipped and unzipped. It provides automated and efficient +signal processing for untargeted NMR metabolomics. It is able to interpolate +the samples, detect outliers, exclude regions, normalize, detect peaks, align +the spectra, integrate peaks, manage metadata and visualize the spectra. +After spectra processing, it can apply multivariate analysis on extracted +data. Efficient plotting with 1-D data is also available. Basic reading of +1D ACD/Labs exported JDX samples is also available.") + (license license:expat))) + (define-public r-altcdfenvs (package (name "r-altcdfenvs") @@ -3480,6 +3706,40 @@ of Bioconductor.") packages.") (license license:artistic2.0))) +(define-public r-breakpointr + (package + (name "r-breakpointr") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "breakpointR" version)) + (sha256 + (base32 + "0j1f43lhgkapjyxlil9fflqh9nf3andhmvirdcv45y60wvljn4gx")))) + (properties `((upstream-name . "breakpointR"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-breakpointrdata + r-cowplot + r-doparallel + r-foreach + r-genomeinfodb + r-genomicalignments + r-genomicranges + r-ggplot2 + r-gtools + r-iranges + r-rsamtools + r-s4vectors)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/daewoooo/BreakPointR") + (synopsis "Find breakpoints in Strand-seq data") + (description + "This package implements functions for finding breakpoints, plotting and +export of Strand-seq data.") + (license license:expat))) + (define-public r-cardelino (package (name "r-cardelino") @@ -4318,6 +4578,37 @@ domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.") (license license:gpl2+))) +(define-public r-italics + (package + (name "r-italics") + (version "2.58.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ITALICS" version)) + (sha256 + (base32 "0g937h9zxkxnm424wh58b46mfasdd7pqy5c04r0a46mx9lxibgbs")))) + (properties `((upstream-name . "ITALICS"))) + (build-system r-build-system) + (propagated-inputs + (list r-affxparser + r-dbi + r-glad + r-italicsdata + r-oligo + r-oligoclasses + r-pd-mapping50k-xba240)) + (home-page "http://bioinfo.curie.fr") + (synopsis "Normalizing of the Affymetrix GeneChip human mapping") + (description + "This package provides tools for normalizing and analyzing of GeneChip +Mapping 100K and 500K Set. Affymetrix GeneChip Human Mapping 100K and 500K +Set allows the DNA copy number mea- surement of respectively 2× 50K and 2× +250K SNPs along the genome. Their high density allows a precise localization +of genomic alterations and makes them a powerful tool for cancer and copy +number polymorphism study.") + (license license:gpl2))) + ;; This is a CRAN package, but it depends on r-biobase and r-limma from Bioconductor. (define-public r-absfiltergsea (package @@ -5973,6 +6264,30 @@ GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome.") (license license:artistic2.0))) +(define-public r-glad + (package + (name "r-glad") + (version "2.62.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "GLAD" version)) + (sha256 + (base32 + "0gb52ic5r6nkgm2ynm174vcvbmkbhhjgv71lsmxpxzcsb6rr7qj6")))) + (properties `((upstream-name . "GLAD"))) + (build-system r-build-system) + (inputs (list gsl)) + (propagated-inputs (list r-aws)) + (native-inputs (list pkg-config)) + (home-page "http://bioinfo.curie.fr") + (synopsis "Gain and loss analysis of DNA") + (description + "This package helps with the analysis of array @acronym{CGH, comparative +genomic hybridization} data by detecting of the breakpoints in the genomic +profiles and assignment of a status (gain, normal or loss) to each chromosomal +regions identified.") + (license license:gpl2))) + (define-public r-gostats (package (name "r-gostats") @@ -6274,6 +6589,61 @@ containing the location/probe set membership mapping. The other one creates a package that automatically loads that environment.") (license license:gpl2+))) +(define-public r-manor + (package + (name "r-manor") + (version "1.70.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "MANOR" version)) + (sha256 + (base32 "16b30bmyzml97cjdbh6h9ky5c4h5ws2a3g2xkxnd55sd3jg64jgx")))) + (properties `((upstream-name . "MANOR"))) + (build-system r-build-system) + (propagated-inputs (list r-glad)) + (native-inputs (list r-knitr)) + (home-page "http://bioinfo.curie.fr/projects/manor/index.html") + (synopsis "CGH micro-array normalization") + (description + "This package ofers functions for importation, normalization, +visualization, and quality control to correct identified sources of +variability in array of @acronym{CGH, comparative genomic hybridization} +experiments.") + (license license:gpl2))) + +(define-public r-maser + (package + (name "r-maser") + (version "1.16.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "maser" version)) + (sha256 + (base32 + "1zycx8s046g4d3w5qrn950bmi0nrnq1g7fvqji48mr6hmsyzplvv")))) + (properties `((upstream-name . "maser"))) + (build-system r-build-system) + (propagated-inputs + (list r-biocgenerics + r-data-table + r-dplyr + r-dt + r-genomeinfodb + r-genomicranges + r-ggplot2 + r-gviz + r-iranges + r-reshape2 + r-rtracklayer)) + (native-inputs (list r-knitr)) + (home-page "https://github.com/DiogoVeiga/maser") + (synopsis "Mapping alternative splicing events to proteins") + (description + "This package provides functionalities for downstream analysis, annotation +and visualizaton of alternative splicing events generated by rMATS.") + (license license:expat))) + (define-public r-metaneighbor (package (name "r-metaneighbor") @@ -6664,6 +7034,73 @@ proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.") (license license:artistic2.0))) +;; This is a CRAN package, but it depends on a Bioconductor package. +(define-public r-numbat + (package + (name "r-numbat") + (version "1.2.1") + (source (origin + (method url-fetch) + (uri (cran-uri "numbat" version)) + (sha256 + (base32 + "1jkz24j99cd333mvisp8x5swwr0iyix1kc962d2yx3mv5cn28xdb")))) + (properties `((upstream-name . "numbat"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-catools + r-data-table + r-dendextend + r-dplyr + r-genomicranges + r-ggplot2 + r-ggraph + r-ggtree + r-glue + r-igraph + r-iranges + r-logger + r-magrittr + r-matrix + r-optparse + r-paralleldist + r-patchwork + r-pryr + r-purrr + r-r-utils + r-rcpp + r-rcpparmadillo + r-rhpcblasctl + r-roptim + r-scales + r-scistreer + r-stringr + r-tibble + r-tidygraph + r-tidyr + r-vcfr + r-zoo)) + (home-page "https://github.com/kharchenkolab/numbat") + (synopsis "Haplotype-aware CNV analysis from scRNA-Seq") + (description + "This package provides a computational method that infers copy number +variations (CNV) in cancer scRNA-seq data and reconstructs the tumor +phylogeny. It integrates signals from gene expression, allelic ratio, and +population haplotype structures to accurately infer allele-specific CNVs in +single cells and reconstruct their lineage relationship. It does not require +tumor/normal-paired DNA or genotype data, but operates solely on the donor +scRNA-data data (for example, 10x Cell Ranger output). It can be used to: + +@enumerate +@item detect allele-specific copy number variations from single-cells +@item differentiate tumor versus normal cells in the tumor microenvironment +@item infer the clonal architecture and evolutionary history of profiled tumors +@end enumerate + +For details on the method see @url{https://doi.org/10.1038/s41587-022-01468-y, +Gao et al in Nature Biotechnology 2022}.") + (license license:expat))) + (define-public r-organism-dplyr (package (name "r-organism-dplyr") @@ -7311,6 +7748,43 @@ includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.") (license license:gpl3))) +;; This is a CRAN package, but it depends on packages from Bioconductor. +(define-public r-scistreer + (package + (name "r-scistreer") + (version "1.1.0") + (source (origin + (method url-fetch) + (uri (cran-uri "scistreer" version)) + (sha256 + (base32 + "0cdp26ngfp5rxa21nqnj6j2098f6996368g4msb3shh7n75np4s9")))) + (properties `((upstream-name . "scistreer"))) + (build-system r-build-system) + (propagated-inputs (list r-ape + r-dplyr + r-ggplot2 + r-ggtree + r-igraph + r-paralleldist + r-patchwork + r-phangorn + r-rcpp + r-rcpparmadillo + r-rcppparallel + r-reshape2 + r-rhpcblasctl + r-stringr + r-tidygraph)) + (home-page "https://github.com/kharchenkolab/scistreer") + (synopsis "Maximum-likelihood perfect phylogeny Inference at scale") + (description + "This package provides fast maximum-likelihood phylogeny inference from +noisy single-cell data using the ScisTree algorithm proposed by +@code{doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019)}. It makes the +method applicable to massive single-cell datasets (>10,000 cells).") + (license license:gpl3))) + (define-public r-scmap (package (name "r-scmap") @@ -7592,6 +8066,34 @@ includes a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.") (license license:gpl3))) +(define-public r-scds + (package + (name "r-scds") + (version "1.14.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "scds" version)) + (sha256 + (base32 + "0zdf9yf5s0l8ma7d8yhi7bjd964yj84f5h6aq2p0sypjlnc515hd")))) + (properties `((upstream-name . "scds"))) + (build-system r-build-system) + (propagated-inputs (list r-dplyr + r-matrix + r-proc + r-s4vectors + r-singlecellexperiment + r-summarizedexperiment + r-xgboost)) + (native-inputs (list r-knitr)) + (home-page "https://bioconductor.org/packages/scds") + (synopsis "In-silico doublet annotation for single cell RNA sequencing data") + (description + "This is an R package for doublet annotation of single cell RNA +sequencing data. @code{scds} provides methods to annotate doublets in +scRNA-seq data computationally.") + (license license:expat))) + (define-public r-slingshot (package (name "r-slingshot") @@ -7624,6 +8126,46 @@ events and allows for the incorporation of prior knowledge through supervised graph construction.") (license license:artistic2.0))) +;; This is a CRAN package but it depends on a bioconductor package. +(define-public r-speaq + (package + (name "r-speaq") + (version "2.7.0") + (source (origin + (method url-fetch) + (uri (cran-uri "speaq" version)) + (sha256 + (base32 + "0z9a3nbfazphp090c6hg892vjq7jp4g4cij3s5wbs1q567inbmlk")))) + (properties `((upstream-name . "speaq"))) + (build-system r-build-system) + (propagated-inputs + (list r-cluster + r-data-table + r-dosnow + r-foreach + r-ggplot2 + r-gridextra + r-impute + r-massspecwavelet + r-missforest + r-reshape2 + r-rfast + r-rvest + r-xml2)) + (native-inputs (list r-knitr)) + (home-page "https://cran.r-project.org/package=speaq") + (synopsis "Tools for nuclear magnetic resonance spectra alignment") + (description + "This package aims to make @acronym{NMR, Nuclear Magnetic Resonance} +spectroscopy data analysis as easy as possible. It only requires a small set +of functions to perform an entire analysis. Speaq offers the possibility of +raw spectra alignment and quantitation but also an analysis based on features +whereby the spectra are converted to peaks which are then grouped and turned +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-stager (package (name "r-stager") @@ -8267,6 +8809,33 @@ 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-quantsmooth + (package + (name "r-quantsmooth") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "quantsmooth" version)) + (sha256 + (base32 "1adwws3brb01d4g6yidipnd8akkiyc3gpdr876hy57qnmcq8xipp")))) + (properties `((upstream-name . "quantsmooth"))) + (build-system r-build-system) + (propagated-inputs (list r-quantreg)) + (home-page "https://bioconductor.org/packages/quantsmooth") + (synopsis "Quantile smoothing and genomic visualization of array data") + (description + "This package implements quantile smoothing. It contains a dataset used +to produce human chromosomal ideograms for plotting purposes and a collection +of arrays that contains data of chromosome 14 of 3 colorectal tumors. The +package provides functions for painting chromosomal icons, chromosome or +chromosomal idiogram and other types of plots. Quantsmooth offers options +like converting chromosomal ids to their numeric form, retrieving the human +chromosomal length from NCBI data, retrieving regions of interest in a vector +of intensities using quantile smoothing, determining cytoband position based +on the location of the probe, and other useful tools.") + (license license:gpl2))) + (define-public r-qvalue (package (name "r-qvalue") @@ -14489,6 +15058,47 @@ be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).") (license license:gpl2))) +(define-public r-tilingarray + (package + (name "r-tilingarray") + (version "1.76.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "tilingArray" version)) + (sha256 + (base32 + "19bkgblpkcp3w3sdyn82c37gkz1sv3r4d546zpbnh36q2pi3l4zd")))) + (properties `((upstream-name . "tilingArray"))) + (build-system r-build-system) + (propagated-inputs + (list r-affy + r-biobase + r-genefilter + r-pixmap + r-rcolorbrewer + r-strucchange + r-vsn)) + (home-page "https://bioconductor.org/packages/tilingArray") + (synopsis "Transcript mapping with high-density oligonucleotide tiling arrays") + (description + "The package provides functionality that can be useful for the analysis +of the high-density tiling microarray data (such as from Affymetrix genechips) +or for measuring the transcript abundance and the architecture. The main +functionalities of the package are: + +@enumerate +@item the class segmentation for representing partitionings of a linear series + of data; +@item the function segment for fitting piecewise constant models using a + dynamic programming algorithm that is both fast and exact; +@item the function @code{confint} for calculating confidence intervals using + the @code{strucchange} package; +@item the function @code{plotAlongChrom} for generating pretty plots; +@item the function @code{normalizeByReference} for probe-sequence dependent + response adjustment from a (set of) reference hybridizations. +@end enumerate") + (license license:artistic2.0))) + (define-public r-timeseriesexperiment (package (name "r-timeseriesexperiment") @@ -16543,6 +17153,26 @@ variety of commonly used matrix types, including sparse and HDF5-backed matrices.") (license license:gpl3))) +(define-public r-beadarraysnp + (package + (name "r-beadarraysnp") + (version "1.64.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "beadarraySNP" version)) + (sha256 + (base32 "06hy89pclbyxjw5yf5i9bc3wr789b9pmhd9sdchgljlijs9vcj6g")))) + (properties `((upstream-name . "beadarraySNP"))) + (build-system r-build-system) + (propagated-inputs (list r-biobase r-quantsmooth)) + (home-page "https://bioconductor.org/packages/beadarraySNP") + (synopsis "Normalization and reporting of Illumina SNP bead arrays") + (description + "This package is importing data from Illumina SNP experiments and it +performs copy number calculations and reports.") + (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. @@ -17674,6 +18304,34 @@ integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.") (license license:gpl3+))) +(define-public r-snapcgh + (package + (name "r-snapcgh") + (version "1.68.0") + (source (origin + (method url-fetch) + (uri (bioconductor-uri "snapCGH" version)) + (sha256 + (base32 + "1zxvl8mkby7yb5kppddag6k9w78d1fm6adx52h4cgrfckn28w64q")))) + (properties `((upstream-name . "snapCGH"))) + (build-system r-build-system) + (propagated-inputs + (list r-acgh + r-cluster + r-dnacopy + r-glad + r-limma + r-tilingarray)) + (home-page "https://bioconductor.org/packages/snapCGH") + (synopsis "Segmentation, normalisation and processing of the aCGH data") + (description + "This package provides methods for segmenting, normalising and processing +aCGH data. snapCGH also includes plotting functions for visualising raw and +segmented data for individual and multiple arrays.") + ;; Expanded from GPL + (license (list license:gpl2+ license:gpl3+)))) + (define-public r-snpstats (package (name "r-snpstats") |