GenomeInfoDb
Utilities for manipulating chromosome names, including modifying them to follow a particular naming style
Bioconductor version: 3.23 · Package version: 1.48.0
Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomeInfoDb")Details
| Maintainer | Hervé Pagès <hpages.on.github@gmail.com> |
| Author | Sonali Arora [aut], Martin Morgan [aut], Marc Carlson [aut], Hervé Pagès [aut, cre], Prisca Chidimma Maduka [ctb], Atuhurira Kirabo Kakopo [ctb], Haleema Khan [ctb] (vignette translation from Sweave to Rmarkdown / HTML), Emmanuel Chigozie Elendu [ctb] |
| License | Artistic-2.0 |
| URL | https://bioconductor.org/packages/GenomeInfoDb |
| Bug Reports | https://github.com/Bioconductor/GenomeInfoDb/issues |
| Downloads rank | 44685 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software |
Documentation
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Dependencies
Depends: R (>= 4.0.0), methods, BiocGenerics (>= 0.53.2), S4Vectors (>= 0.47.6), IRanges (>= 2.41.1), Seqinfo (>= 0.99.2)
Imports: stats, utils, UCSC.utils
Suggests: GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocStyle, knitr
Reverse dependencies
Depends On Me (10): annotation, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenomeForge, CODEX, IdeoViz, liftOver, SCOPE, UCSCRepeatMasker, variants
Imports Me (200): ActiveDriverWGS, AllelicImbalance, annoLinker, AnnotationHubData, atacInferCnv, ATACseqQC, atena, BaalChIP, bambu, Banksy, bedbaser, BindingSiteFinder, biovizBase, biscuiteer, breakpointR, BUSpaRse, cageminer, cardelino, cfdnakit, cfDNAPro, chimeraviz, ChIPanalyser, chipenrich.data, ChIPpeakAnno, ChIPseeker, circRNAprofiler, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, comapr, CopyNumberPlots, crisprDesign, crispRdesignR, CrispRVariants, customProDB, damidBind, Damsel, derfinder, derfinderPlot, DEScan2, DESNP, diffHic, diffUTR, DMRcaller, DOTSeq, driveR, DuplexDiscovereR, easylift, ensembldb, EpiCompare, epigenomix, epimutacions, epiregulon, epiRomics, epiSeeker, epivizr, EventPointer, extraChIPs, factR, fastRanges, fitCons.UCSC.hg19, fourSynergy, fRagmentomics, FRASER, funtooNorm, GA4GHshiny, gDNAx, GenomicDistributions, GenomicDistributionsData, GenomicFiles, GenomicPlot, GenomicScores, ggbio, GOaGO, GRaNIE, grasp2db, GUIDEseq, Gviz, gwascat, h5vc, HiCaptuRe, HiCDCPlus, HiContacts, hicream, idr2d, igblastr, InPAS, karyoploteR, karyotapR, katdetectr, linkSet, locuszoomr, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v4.0.GRCh38, mariner, metagene2, metaseqR2, methimpute, methodical, MethylSeekR, MethylSeqData, methylumi, missMethyl, mobileRNA, Motif2Site, motifbreakR, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, normr, ocrRBBR, OGRE, ORFik, parati, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, plotgardener, proActiv, profileplyr, ProteoDisco, PureCN, R3CPET, raer, RareVariantVis, RCAS, RcisTarget, recount, regioneR, regionReport, RESOLVE, revert, rGREAT, ribosomeProfilingQC, roar, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, SEMPLR, seqCAT, SGSeq, Signac, signeR, SigsPack, Site2Target, SNPhood, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, SOMNiBUS, SparseSignatures, SPICEY, spiky, SpliceWiz, STADyUM, StructuralVariantAnnotation, svaNUMT, svaRetro, TAPseq, TCGAutils, tepr, tidyCoverage, TmCalculator, TnT, trackViewer, transcriptR, txdbmaker, Ularcirc, UMI4Cats, UPDhmm, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me (76): AlphaMissenseR, AnnotationForge, AnnotationHub, annotatr, BgeeCall, BioMartGOGeneSets, BSgenome, bumphunter, Chicago, CNVScope, crupR, CTCF, dar, DEXSeq, DFplyr, DiffBind, DMRcate, enhancerHomologSearch, epialleleR, epigraHMM, excluderanges, ExperimentHubData, fishpond, GA4GHclient, GENESIS, GenomicFeatures, GenomicRanges, GenomicTuples, gkmSVM, gmapR, gmoviz, GRIN2, gwas2crispr, HelloRanges, HicAggR, icetea, jazzPanda, LACHESIS, ldblock, megadepth, methrix, multicrispr, nullranges, Organism.dplyr, OUTRIDER, parglms, peakCombiner, PICB, PlinkMatrix, plyinteractions, polyRAD, QDNAseq, RaggedExperiment, RapidoPGS, recoup, regioneReloaded, rtracklayer, scGraphVerse, scLANE, scTreeViz, Seqinfo, seqpac, seqsetvis, sesame, sesameData, Seurat, sitadela, SomaticSignatures, splatter, SummarizedExperiment, systemPipeR, TEKRABber, treeclimbR, UCSC.utils, VariantAnnotation, xcoredata