GenomeInfoDb

DOI: 10.18129/B9.bioc.GenomeInfoDb    

This is the development version of GenomeInfoDb; for the stable release version, see GenomeInfoDb.

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

Bioconductor version: Development (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

 

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

Details

biocViews	Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version	1.23.0
In Bioconductor since	BioC 2.14 (R-3.1) (5.5 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
LinkingTo
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
SystemRequirements
Enhances
URL
Depends On Me	BSgenome, bumphunter, ChIPComp, CODEX, CSAR, eQTL, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, IdeoViz, methyAnalysis, MTseeker, Rsamtools, SNPlocs.Hsapiens.dbSNP141.GRCh38, SNPlocs.Hsapiens.dbSNP142.GRCh37, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me	AllelicImbalance, alpine, amplican, AneuFinder, AnnotationHubData, annotatr, ASpediaFI, ATACseqQC, BaalChIP, ballgown, BasicSTARRseq, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, BSgenome, bsseq, BUSpaRse, CAGEfightR, CAGEr, casper, CexoR, chimeraviz, ChIPanalyser, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, circRNAprofiler, cleanUpdTSeq, cn.mops, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, compEpiTools, consensusSeekeR, conumee, CopyNumberPlots, CopywriteR, CrispRVariants, csaw, customProDB, DeepBlueR, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffloop, DMRcate, DMRScan, dmrseq, DominoEffect, easyRNASeq, ELMER, ENCODExplorer, enrichTF, ensembldb, ensemblVEP, epigenomix, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, exomeCopy, fitCons.UCSC.hg19, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicFiles, GenomicInteractions, GenomicOZone, GenomicScores, GenomicState, genoset, genotypeeval, GenVisR, ggbio, GGtools, GOTHiC, gQTLstats, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiCBricks, HiTC, HTSeqGenie, idr2d, IMAS, InPAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MACPET, MADSEQ, 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.gnomAD.r3.0.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, maser, metagene, metagene2, metavizr, MethCP, methimpute, methInheritSim, methylKit, methylPipe, methylumi, methyvim, minfi, MinimumDistance, MMAPPR2, mosaics, motifbreakR, motifmatchr, msgbsR, MTseekerData, multiHiCcompare, MutationalPatterns, myvariant, NADfinder, NarrowPeaks, normr, nucleR, OMICsPCA, ORFik, Organism.dplyr, panelcn.mops, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38, Pi, pipeFrame, plyranges, podkat, pram, prebs, profileplyr, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RaggedExperiment, RareVariantVis, Rariant, Rcade, RCAS, rCGH, recount, regioneR, regionReport, REMP, Repitools, RiboProfiling, riboSeqR, RJMCMCNucleosomes, RNAmodR, roar, RTCGAToolbox, rtracklayer, scmeth, scruff, segmentSeq, SeqArray, seqCAT, seqplots, seqsetvis, sevenC, SGSeq, ShortRead, signeR, SigsPack, 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, strandCheckR, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TCGAutils, TCGAWorkflow, TFBSTools, TitanCNA, TnT, trackViewer, transcriptR, tRNAscanImport, TSRchitect, TVTB, tximeta, TxRegInfra, Ularcirc, 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, methrix, parglms, QDNAseq, recoup, StructuralVariantAnnotation, TFutils
Links To Me
Build Report

Package Archives

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

Source Package	GenomeInfoDb_1.23.0.tar.gz
Windows Binary	GenomeInfoDb_1.23.0.zip
Mac OS X 10.11 (El Capitan)	GenomeInfoDb_1.23.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomeInfoDb
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomeInfoDb
Package Short Url	https://bioconductor.org/packages/GenomeInfoDb/
Package Downloads Report	Download Stats