GenomeInfoDb

This is the released version of GenomeInfoDb; for the devel version, see GenomeInfoDb.

Utilities for manipulating chromosome names, including modifying them to follow a particular naming style

Bioconductor version: Release (3.23)

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.

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]

Maintainer: Hervé Pagès <hpages.on.github at gmail.com>

Citation (from within R, enter citation("GenomeInfoDb")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("GenomeInfoDb")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GenomeInfoDb")

GenomeInfoDb: Introduction to GenomeInfoDb	PDF	R Script
Submitting your organism to GenomeInfoDb	HTML	R Script
Reference Manual	PDF
NEWS	Text
- YouTube	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version	1.48.0
In Bioconductor since	BioC 2.14 (R-3.1) (12.5 years)
License	Artistic-2.0
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
System Requirements
URL	https://bioconductor.org/packages/GenomeInfoDb
Bug Reports	https://github.com/Bioconductor/GenomeInfoDb/issues

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
Linking To
Enhances
Depends On Me	BSgenomeForge, CODEX, IdeoViz, SCOPE, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, UCSCRepeatMasker, annotation, liftOver, variants
Imports Me	AllelicImbalance, annoLinker, AnnotationHubData, atacInferCnv, ATACseqQC, atena, BaalChIP, bambu, Banksy, bedbaser, BindingSiteFinder, biovizBase, biscuiteer, breakpointR, BUSpaRse, cageminer, cardelino, cfdnakit, cfDNAPro, chimeraviz, ChIPpeakAnno, ChIPseeker, circRNAprofiler, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, comapr, CopyNumberPlots, crisprDesign, CrispRVariants, customProDB, damidBind, Damsel, derfinder, derfinderPlot, DEScan2, diffHic, diffUTR, DMRcaller, DOTSeq, DuplexDiscovereR, easylift, ensembldb, EpiCompare, epigenomix, epimutacions, epiregulon, epiRomics, epiSeeker, epivizr, EventPointer, extraChIPs, factR, fastRanges, fourSynergy, fRagmentomics, FRASER, funtooNorm, GA4GHshiny, gDNAx, GenomicDistributions, GenomicFiles, GenomicPlot, GenomicScores, ggbio, GOaGO, GRaNIE, GUIDEseq, Gviz, gwascat, h5vc, HiCaptuRe, HiContacts, idr2d, igblastr, karyoploteR, katdetectr, mariner, metagene2, metaseqR2, methimpute, methodical, MethylSeekR, methylumi, missMethyl, mobileRNA, Motif2Site, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, normr, OGRE, ORFik, parati, plotgardener, proActiv, profileplyr, ProteoDisco, PureCN, R3CPET, raer, RareVariantVis, RCAS, recount, regioneR, regionReport, RESOLVE, rGREAT, ribosomeProfilingQC, roar, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, SEMPLR, seqCAT, SGSeq, signeR, SigsPack, Site2Target, SNPhood, SOMNiBUS, SparseSignatures, SPICEY, spiky, SpliceWiz, STADyUM, svaNUMT, svaRetro, TAPseq, TCGAutils, tidyCoverage, TnT, trackViewer, transcriptR, txdbmaker, UMI4Cats, UPDhmm, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, fitCons.UCSC.hg19, grasp2db, 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, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP155.GRCh37, SNPlocs.Hsapiens.dbSNP155.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, chipenrich.data, GenomicDistributionsData, MethylSeqData, OSTA, ActiveDriverWGS, crispRdesignR, DESNP, driveR, hicream, karyotapR, locuszoomr, ocrRBBR, revert, Signac, tepr, TmCalculator
Suggests Me	AlphaMissenseR, AnnotationForge, AnnotationHub, annotatr, BgeeCall, BSgenome, bumphunter, Chicago, crupR, dar, DEXSeq, DFplyr, DiffBind, DMRcate, enhancerHomologSearch, epialleleR, epigraHMM, ExperimentHubData, fishpond, GA4GHclient, GENESIS, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, gmoviz, HelloRanges, HicAggR, icetea, jazzPanda, LACHESIS, ldblock, megadepth, methrix, multicrispr, nullranges, OUTRIDER, parglms, peakCombiner, PICB, PlinkMatrix, plyinteractions, QDNAseq, RaggedExperiment, recoup, regioneReloaded, rtracklayer, scGraphVerse, scLANE, scTreeViz, Seqinfo, seqsetvis, sesame, sitadela, SomaticSignatures, splatter, SummarizedExperiment, systemPipeR, TEKRABber, treeclimbR, UCSC.utils, VariantAnnotation, BioMartGOGeneSets, CTCF, excluderanges, sesameData, xcoredata, seqpac, gkmSVM, GRIN2, gwas2crispr, polyRAD, RapidoPGS, Seurat
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GenomeInfoDb_1.48.0.tar.gz
Windows Binary (x86_64)	GenomeInfoDb_1.48.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	GenomeInfoDb_1.48.0.tgz
macOS Binary (sonoma-arm64)	GenomeInfoDb_1.48.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomeInfoDb
Bioc Package Browser	https://code.bioconductor.org/browse/GenomeInfoDb/
Package Short Url	https://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report	Download Stats