CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Maintainer:Julie Aubert, Toby Dylan Hocking, Nathalie Vialaneix
Contact:julie.aubert at inrae.fr
Version:2024-04-04
URL:https://CRAN.R-project.org/view=Omics
Source:https://github.com/cran-task-views/Omics/
Contributions:Suggestions and improvements for this task view are very welcome and can be made through issues or pull requests on GitHub or via e-mail to the maintainer address. For further details see the Contributing guide.
Citation:Julie Aubert, Toby Dylan Hocking, Nathalie Vialaneix (2024). CRAN Task View: Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics. Version 2024-04-04. URL https://CRAN.R-project.org/view=Omics.
Installation:The packages from this task view can be installed automatically using the ctv package. For example, ctv::install.views("Omics", coreOnly = TRUE) installs all the core packages or ctv::update.views("Omics") installs all packages that are not yet installed and up-to-date. See the CRAN Task View Initiative for more details.

In this task view, we focus on the most-important CRAN packages dedicated to omics data analysis including those related to annotation and databases. The term omics concerns various biological disciplines ending with the suffix -omics, such as genomics, proteomics, metabolomics, transcriptomics. We include CRAN packages which have been published more than one year ago and are regularly updated. Therefore, very recent packages may not appear yet but may be included soon if they are maintained. A few additional packages from the Bioconductor project are included, not looking for an exhaustive description but pointing to the must-see packages or to packages focused on omics not well covered by CRAN packages. Complementary information might also be found in Phylogenetics, MachineLearning, Agriculture or MissingData task views. Note that packages covering statistical genetics data (DNA data, haplotype estimation, population structure, genetic epidemiology), phylogenetics and phylogenomics are not covered by this task view. Still further packages might be found on Bioconductor, R-Forge, and GitHub.

If you think we have missed some important packages in this list, please e-mail the maintainers or submit an issue or pull request in the GitHub repository linked above.

The task view is structured into main topics:

Annotation and databases

Genomics

Transcriptomics

Microarray or other continuous expression data

RNA-seq data

Single-cell RNA-seq

Proteomics

Metabolomics

Other omics

Multiple omics

Specific tasks

Quality control and normalization

Peak calling and analysis in data like ChIP-seq and ATAC-seq

Multiple testing

High-dimensional data regularization

Networks

Clustering

Visualization

Missing values

Specific application fields

CRAN packages

Core:aLFQ, biomartr, ChemoSpec, GeneNet, GenomicTools.fileHandler, o2plsda, pagoda2, PMA, Seurat, WebGestaltR, WGCNA, wrProteo.
Regular:ACNE, ActivePathways, ADAPTS, adjclust, agvgd, alakazam, aliases2entrez, ampir, AnaCoDa, AnnotationBustR, aroma.cn, babelgene, BarcodingR, BASiNET, bayefdr, BClustLonG, BED, BiasCorrector, bio3d, BioInsight, bioseq, BisqueRNA, BRINDA, Cascade, CascadeData, CB2, cbioportalR, CePa, CeRNASeek, chromoMap, clustermole, compas, conos, CovCombR, cp4p, cubfits, cumSeg, depthTools, desiR, DGEobj, DGEobj.utils, DiffCorr, diffEnrich, DiPALM, directPA, DIscBIO, DiscreteFDR, dnapath, DRaWR, driveR, DRomics, dsb, dynwrap, DysPIA, DysPIAData, EMMIXgene, enrichR, enveomics.R, erah, fbar, FiRE, flippant, ftrCOOL, func2vis, GANPA, GANPAdata, GeneCycle, geneExpressionFromGEO, geno2proteo, genoPlotR, gggenes, glmmSeq, GOxploreR, gprofiler2, graphsim, GSA, hgnc, hommel, hsstan, HTSCluster, ICAMS, iCARH, ICBioMark, ICDS, iCellR, IMIX, immunarch, imp4p, imputeLCMD, imsig, integIRTy, InteRD, interep, ioncopy, iq, JBrowseR, JSparO, KRIS, krm, leapp, liger, lilikoi, lineup, lineup2, lmQCM, LPS, LSPFP, LUCIDus, MAAPER, maGUI, Map2NCBI, markerpen, MCMC.qpcr, metaboData, MetabolicSurv, MetabolomicsBasics, MetaIntegrator, metaMA, metaRNASeq, MetSizeR, mi4p, miic, MINTplates, MiRNAQCD, MOSS, mpm, mpmi, msigdbr, mutSignatures, NACHO, nanostringr, NBBttest, NBPSeq, net4pg, netgsa, networkABC, NewmanOmics, OmicNavigator, omicwas, omu, oncoPredict, optBiomarker, OptCirClust, ORIClust, packMBPLSDA, parmigene, pathfindR, pathfindR.data, pathwayTMB, Patterns, pbm, PeakError, PeakSegDisk, PeakSegJoint, PeakSegOptimal, permPATH, phateR, pinfsc50, PINSPlus, POD, popPCR, PQLseq, PredCRG, prioGene, prioritylasso, protti, protViz, prozor, PSCBS, PSSMCOOL, ptm, PTXQC, RAMClustR, rBiasCorrection, RCircos, RcmdrPlugin.depthTools, read.gb, Rediscover, regnet, RGBM, RHclust, riceidconverter, RIdeogram, RNAseqNet, RNAsmc, RNentropy, RobustRankAggreg, rPanglaoDB, rSEA, RVA, scBio, sccore, scINSIGHT, scLink, scoper, SCORPIUS, scSorter, scTenifoldKnk, scTenifoldNet, semmcmc, seqgendiff, seqinr, SeqNet, SeuratObject, SIBERG, sigminer, Signac, SignacX, sigora, SIMMS, singleCellHaystack, SlaPMEG, slfm, SMDIC, SMVar, solvebio, sonicLength, SoupX, ssize.fdr, statVisual, stochprofML, supclust, SurrogateRegression, survival666, TailRank, TCA, TcGSA, TGS, tidyestimate, tinyarray, Tmisc, tmod, topologyGSA, toprdata, treefit, VALERIE, valr, VAM, vhica, volcano3D, whitening, wilson, wrMisc, ypssc.

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