GenomeInfoDb

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see GenomeInfoDb.

Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: 3.7

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, Martin Morgan, Marc Carlson, H. Pagès

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

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

Installation

To install this package, start R (version "3.5") 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
GenomeInfoDb: Submitting your organism to GenomeInfoDb	PDF	R Script
Reference Manual	PDF
NEWS	Text
Simple tasks genomeInfoDb	Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version	1.16.0
In Bioconductor since	BioC 2.14 (R-3.1) (10 years)
License	Artistic-2.0
Depends	R (>= 3.1), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.17.25), IRanges(>= 2.13.12)
Imports	stats, stats4, utils, RCurl, GenomeInfoDbData
System Requirements
URL

Suggests	GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr
Linking To
Enhances
Depends On Me	BSgenome, bumphunter, ChIPComp, CODEX, CSAR, eQTL, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, htSeqTools, IdeoViz, methyAnalysis, Rsamtools, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me	AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ATACseqQC, BaalChIP, ballgown, BasicSTARRseq, biovizBase, BiSeq, bnbc, branchpointer, BSgenome, bsseq, CAGEfightR, CAGEr, casper, CexoR, chimeraviz, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, cn.mops, CNEr, CNPBayes, CNVPanelizer, compEpiTools, consensusSeekeR, conumee, CopywriteR, CrispRVariants, csaw, customProDB, DeepBlueR, derfinder, derfinderPlot, DEScan2, diffHic, diffloop, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, ensembldb, ensemblVEP, epigenomix, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, fitCons.UCSC.hg19, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicFiles, GenomicInteractions, GenomicScores, genoset, genotypeeval, GenVisR, ggbio, GGtools, GoogleGenomics, gQTLstats, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiTC, HTSeqGenie, IMAS, InPAS, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MACPET, MADSEQ, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.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.r2.0.1.GRCh38, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.GRCh38, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, metagene, metavizr, methimpute, methInheritSim, methylKit, methylPipe, methylumi, methyvim, minfi, MinimumDistance, mosaics, motifbreakR, motifmatchr, msgbsR, MutationalPatterns, myvariant, NADfinder, NarrowPeaks, normr, nucleR, ORFik, Organism.dplyr, panelcn.mops, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, plyranges, podkat, prebs, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RareVariantVis, Rariant, Rcade, RCAS, rCGH, recount, regioneR, regionReport, Repitools, RiboProfiling, riboSeqR, RJMCMCNucleosomes, roar, RTCGAToolbox, rtracklayer, scmeth, segmentSeq, SeqArray, seqCAT, seqplots, sevenC, SGSeq, ShortRead, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, SNPlocs.Hsapiens.dbSNP149.GRCh38, SNPlocs.Hsapiens.dbSNP150.GRCh38, SNPlocs.Hsapiens.dbSNP151.GRCh38, soGGi, SomaticSignatures, SparseSignatures, SplicingGraphs, SPLINTER, srnadiff, STAN, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TCGAutils, TCGAWorkflow, TFBSTools, TFutils, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, TxRegInfra, VanillaICE, VariantFiltering, VariantTools, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA, yriMulti
Suggests Me	AnnotationForge, AnnotationHub, BiocOncoTK, chromswitch, ExperimentHubData, gQTLBase, QDNAseq, recoup
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	GenomeInfoDb_1.16.0.tar.gz
Windows Binary	GenomeInfoDb_1.16.0.zip
Mac OS X 10.11 (El Capitan)	GenomeInfoDb_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access)	git clone [email protected]:packages/GenomeInfoDb
Package Short Url	https://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.7	Source Archive