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Utilities for manipulating chromosome and other 'seqname' identifiers

Bioconductor version: Release (3.2)

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. Pages

Maintainer: Bioconductor Package Maintainer <maintainer at>

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


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PDF GenomeInfoDb :Introduction to GenomeInfoDb
PDF GenomeInfoDb: Submitting your organism to GenomeInfoDb
PDF   Reference Manual
Text   NEWS
Video   Simple tasks genomeInfoDb


biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software
Version 1.6.1
In Bioconductor since BioC 2.14 (R-3.1) (1.5 years)
License Artistic-2.0
Depends R (>= 3.1), methods, stats4, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.7.11), IRanges(>= 1.99.26)
Imports methods, BiocGenerics, S4Vectors
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
Depends On Me BSgenome, bsseq, bumphunter, ChIPComp, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, htSeqTools, IdeoViz, methyAnalysis, Rsamtools, SNPlocs.Hsapiens.dbSNP142.GRCh37, TitanCNA, VariantAnnotation, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38
Imports Me AllelicImbalance, AnnotationHubData, ballgown, biovizBase, BiSeq, BSgenome, casper, CexoR, ChIPpeakAnno, ChIPseeker, CNEr, CNPBayes, compEpiTools, conumee, CopywriteR, csaw, customProDB, derfinder, derfinderPlot, diffHic, easyRNASeq, ELMER, ensembldb, epivizr, exomeCopy, genomation, genomeIntervals, GenomicInteractions, genoset, genotypeeval, ggbio, GGtools, GoogleGenomics, gQTLstats, grasp2db, GreyListChIP, Gviz, gwascat, h5vc, HiTC, InPAS, IVAS, metagene, methylPipe, methylumi, minfi, MinimumDistance, motifbreakR, myvariant, NarrowPeaks, podkat, prebs, ProteomicsAnnotationHubData, qpgraph, QuasR, r3Cseq, RareVariantVis, Rariant, rCGH, regionReport, Repitools, RiboProfiling, rtracklayer, seqplots, SGSeq, ShortRead, SNPchip, SNPhood, SNPlocs.Hsapiens.dbSNP142.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh37, SNPlocs.Hsapiens.dbSNP144.GRCh38, soGGi, SomaticSignatures, SplicingGraphs, SummarizedExperiment, TarSeqQC, TFBSTools, VanillaICE, VariantFiltering, VariantTools, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38
Suggests Me AnnotationHub, gQTLBase, QDNAseq
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