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Bioconductor - GenomeInfoDb

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 (3.21)

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")): Installation

To install this package, start R (version "4.5") 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")
Details biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software Version 1.44.0 In Bioconductor since BioC 2.14 (R-3.1) (11 years) License Artistic-2.0 Depends R (>= 4.0.0), methods, BiocGenerics(>= 0.53.2), S4Vectors(>= 0.45.2), IRanges(>= 2.41.1) Imports stats, stats4, utils, UCSC.utils, GenomeInfoDbData System Requirements URL https://bioconductor.org/packages/GenomeInfoDb Bug Reports https://github.com/Bioconductor/GenomeInfoDb/issues See More Suggests R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome, 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 Biostrings, BSgenome, BSgenomeForge, bumphunter, CODEX, CSAR, GenomicAlignments, GenomicFeatures, GenomicRanges, GenomicTuples, gmapR, groHMM, HelloRanges, IdeoViz, Rsamtools, SCOPE, txdbmaker, VariantAnnotation, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, UCSCRepeatMasker, RTIGER Imports Me alabaster.ranges, AllelicImbalance, amplican, AneuFinder, AnnotationHubData, annotatr, ATACseqQC, ATACseqTFEA, atena, BaalChIP, ballgown, bambu, bedbaser, BindingSiteFinder, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, bsseq, BUSpaRse, CAGEfightR, cageminer, CAGEr, cardelino, casper, cBioPortalData, CexoR, cfdnakit, cfDNAPro, chimeraviz, chipenrich, ChIPexoQual, ChIPpeakAnno, ChIPseeker, chromVAR, circRNAprofiler, cleanUpdTSeq, CleanUpRNAseq, cn.mops, CNEr, CNVfilteR, CNVPanelizer, CNVRanger, Cogito, comapr, compEpiTools, consensusSeekeR, conumee, CopyNumberPlots, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, CrispRVariants, crisprViz, crupR, csaw, customProDB, DAMEfinder, Damsel, decompTumor2Sig, DegCre, demuxSNP, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easylift, easyRNASeq, ELMER, enhancerHomologSearch, ensembldb, EpiCompare, epigenomix, epigraHMM, EpiMix, epimutacions, epiregulon, EpiTxDb, epivizr, epivizrData, epivizrStandalone, erma, esATAC, EventPointer, extraChIPs, factR, FindIT2, FLAMES, FRASER, funtooNorm, G4SNVHunter, GA4GHclient, GA4GHshiny, gcapc, gDNAx, geneAttribution, genomation, GenomAutomorphism, genomeIntervals, GenomicDistributions, GenomicFiles, GenomicInteractionNodes, GenomicInteractions, GenomicOZone, GenomicPlot, GenomicScores, GenVisR, geomeTriD, ggbio, gmoviz, goseq, GOTHiC, GRaNIE, GreyListChIP, GUIDEseq, Gviz, gwascat, h5vc, heatmaps, HicAggR, HiCBricks, HiCDOC, HiCExperiment, HiContacts, HiCParser, hicVennDiagram, HiTC, idr2d, IMAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, katdetectr, MADSEQ, mariner, maser, metagene2, metaseqR2, methimpute, methInheritSim, methodical, methylKit, methylPipe, methylSig, methylumi, minfi, MinimumDistance, mobileRNA, monaLisa, mosaics, Motif2Site, motifbreakR, motifmatchr, MotifPeeker, motifTestR, MouseFM, msgbsR, multicrispr, multiHiCcompare, MungeSumstats, musicatk, MutationalPatterns, myvariant, NADfinder, nearBynding, normr, nucleR, nullranges, OGRE, OMICsPCA, ORFik, Organism.dplyr, panelcn.mops, periodicDNA, PICB, pipeFrame, plotgardener, plyinteractions, plyranges, podkat, pram, prebs, proActiv, profileplyr, ProteoDisco, PureCN, qpgraph, qsea, QuasR, R3CPET, r3Cseq, raer, RaggedExperiment, ramr, RareVariantVis, RCAS, RcisTarget, recount, recoup, regioneR, regionReport, REMP, Repitools, RESOLVE, rfPred, RgnTX, rGREAT, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, rigvf, RJMCMCNucleosomes, rnaEditr, RNAmodR, roar, RTCGAToolbox, rtracklayer, scanMiR, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, segmentSeq, seqArchRplus, SeqArray, seqCAT, seqsetvis, sesame, sevenC, SGSeq, ShortRead, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, Site2Target, SNPhood, soGGi, SomaticSignatures, SOMNiBUS, SparseSignatures, spatzie, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, SummarizedExperiment, svaNUMT, svaRetro, tadar, TAPseq, TCGAutils, TEKRABber, TENxIO, TFBSTools, tidyCoverage, TitanCNA, TnT, trackViewer, transcriptR, transmogR, tRNAscanImport, TVTB, tximeta, Ularcirc, UMI4Cats, VanillaICE, VariantFiltering, VariantTools, VaSP, VplotR, wiggleplotr, YAPSA, fitCons.UCSC.hg19, GenomicState, 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, BioPlex, chipenrich.data, GenomicDistributionsData, MethylSeqData, sesameData, crispRdesignR, driveR, ICAMS, locuszoomr, MAAPER, Signac, tepr Suggests Me AlphaMissenseR, AnnotationForge, AnnotationHub, DFplyr, DiffBind, epialleleR, ExperimentHubData, fishpond, ldblock, megadepth, methrix, OUTRIDER, parglms, QDNAseq, RAIDS, regioneReloaded, scTreeViz, splatter, systemPipeR, TFutils, UCSC.utils, BioMartGOGeneSets, xcoredata, gkmSVM, GRIN2, polyRAD, Seurat Links To Me Build Report Build Report Package Archives

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