GenomeInfoDb
DOI:
10.18129/B9.bioc.GenomeInfoDb
Utilities for manipulating chromosome and other 'seqname' identifiers
Bioconductor version: Release (3.6)
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 and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomeInfoDb")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("GenomeInfoDb")
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PDF
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R Script
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GenomeInfoDb: Introduction to GenomeInfoDb |
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PDF
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R Script
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GenomeInfoDb: Submitting your organism to GenomeInfoDb |
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PDF
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Reference Manual |
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Text
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NEWS |
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Video
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Simple tasks genomeInfoDb |
Details
| biocViews |
Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software |
| Version |
1.14.0 |
| In Bioconductor since |
BioC 2.14 (R-3.1) (4 years) |
| License |
Artistic-2.0 |
| Depends |
R (>= 3.1), methods, BiocGenerics(>= 0.13.8), S4Vectors(>= 0.9.25), IRanges(>= 1.99.26) |
| Imports |
stats, stats4, utils, RCurl, GenomeInfoDbData |
| LinkingTo |
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| 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 |
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| Enhances |
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| URL |
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| Depends On Me |
BSgenome, bumphunter, ChIPComp, CODEX, CSAR, 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, casper, CexoR, chimeraviz, chipenrich, chipenrich.data, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromstaR, chromVAR, CINdex, cn.mops, CNEr, CNPBayes, compEpiTools, consensusSeekeR, conumee, CopywriteR, CrispRVariants, csaw, customProDB, DeepBlueR, derfinder, derfinderPlot, diffHic, diffloop, easyRNASeq, ELMER, ensembldb, ensemblVEP, epigenomix, epivizrData, epivizrStandalone, esATAC, EventPointer, exomeCopy, FunChIP, funtooNorm, GA4GHclient, GA4GHshiny, gcapc, genbankr, geneAttribution, GenoGAM, genomation, genomeIntervals, GenomicFiles, GenomicInteractions, GenomicScores, genoset, genotypeeval, ggbio, GGtools, GoogleGenomics, gQTLstats, grasp2db, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HiTC, HTSeqGenie, IMAS, InPAS, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, ldblock, MADSEQ, metagene, metavizr, methimpute, methInheritSim, methylKit, methylPipe, methylumi, methyvim, minfi, MinimumDistance, mosaics, motifbreakR, motifmatchr, msgbsR, MutationalPatterns, myvariant, NADfinder, NarrowPeaks, normr, Organism.dplyr, panelcn.mops, Pi, podkat, prebs, ProteomicsAnnotationHubData, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, RareVariantVis, Rariant, Rcade, RCAS, rCGH, recount, regioneR, regionReport, Repitools, RiboProfiling, riboSeqR, RJMCMCNucleosomes, roar, RTCGAToolbox, rtracklayer, segmentSeq, SeqArray, seqCAT, seqplots, 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, soGGi, SomaticSignatures, SplicingGraphs, SPLINTER, STAN, SummarizedExperiment, TarSeqQC, TCGAbiolinks, TFBSTools, TitanCNA, TnT, trackViewer, transcriptR, TSRchitect, TVTB, VanillaICE, VariantFiltering, VariantTools, wiggleplotr, XtraSNPlocs.Hsapiens.dbSNP141.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh37, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, YAPSA, yriMulti |
| Suggests Me |
AnnotationForge, AnnotationHub, ExperimentHubData, gQTLBase, QDNAseq, recoup |
| Build Report |
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Package Archives
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