A RetroSearch Logo

Home - News ( United States | United Kingdom | Italy | Germany ) - Football scores

Search Query:

Showing content from https://bioconductor.org/packages/devel/bioc/html/../../bioc/html/../../bioc/html/GenomeInfoDb.html below:

Bioconductor - GenomeInfoDb (development version)

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 (3.22)

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")

# 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")
Details biocViews Annotation, DataRepresentation, Genetics, GenomeAnnotation, Software Version 1.45.7 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), Seqinfo Imports stats, utils, UCSC.utils System Requirements URL https://bioconductor.org/packages/GenomeInfoDb Bug Reports https://github.com/Bioconductor/GenomeInfoDb/issues See More Suggests GenomeInfoDbData, R.utils, data.table, GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, 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 BSgenomeForge, bumphunter, CODEX, CSAR, gmapR, groHMM, HelloRanges, IdeoViz, SCOPE, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, UCSCRepeatMasker, RTIGER Imports Me alabaster.ranges, AllelicImbalance, AnnotationHubData, ATACseqQC, ATACseqTFEA, atena, BaalChIP, ballgown, bambu, bedbaser, BindingSiteFinder, biovizBase, biscuiteer, BiSeq, bnbc, branchpointer, breakpointR, BUSpaRse, cageminer, cardelino, casper, CexoR, cfdnakit, cfDNAPro, chimeraviz, chipenrich, ChIPpeakAnno, ChIPseeker, chromVAR, circRNAprofiler, cleanUpdTSeq, CleanUpRNAseq, cn.mops, CNVfilteR, CNVPanelizer, CNVRanger, Cogito, comapr, consensusSeekeR, conumee, CopyNumberPlots, crisprBowtie, crisprBwa, crisprDesign, CRISPRseek, crisprShiny, CrispRVariants, crisprViz, crupR, customProDB, DAMEfinder, Damsel, decompTumor2Sig, DegCre, demuxSNP, derfinder, derfinderPlot, DEScan2, DEWSeq, diffHic, diffUTR, DMRcate, DMRScan, dmrseq, DominoEffect, easylift, ELMER, enhancerHomologSearch, ensembldb, EpiCompare, epigenomix, epigraHMM, EpiMix, epimutacions, epiregulon, EpiTxDb, epivizr, epivizrData, epivizrStandalone, 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, igblastr, IMAS, INSPEcT, InteractionSet, IsoformSwitchAnalyzeR, IVAS, karyoploteR, katdetectr, mariner, maser, metagene2, metaseqR2, methimpute, methInheritSim, methodical, methylKit, methylPipe, methylSig, methylumi, 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, panelcn.mops, periodicDNA, PICB, pipeFrame, plotgardener, plyinteractions, plyranges, podkat, pram, prebs, proActiv, profileplyr, ProteoDisco, PureCN, qpgraph, qsea, R3CPET, r3Cseq, raer, RareVariantVis, RCAS, RcisTarget, recount, recoup, regioneR, regionReport, REMP, Repitools, RESOLVE, rfPred, RgnTX, rGREAT, RiboCrypt, RiboProfiling, riboSeqR, ribosomeProfilingQC, rigvf, RJMCMCNucleosomes, rnaEditr, RNAmodR, roar, RTCGAToolbox, scanMiR, scanMiRApp, scDblFinder, scmeth, scRNAseqApp, scruff, segmentSeq, seqArchRplus, SeqArray, seqCAT, seqsetvis, sevenC, SGSeq, ShortRead, signeR, SigsPack, SingleMoleculeFootprinting, sitadela, Site2Target, SNPhood, soGGi, SomaticSignatures, SOMNiBUS, SparseSignatures, spatzie, spiky, SpliceWiz, SplicingGraphs, SPLINTER, srnadiff, strandCheckR, svaNUMT, svaRetro, tadar, TAPseq, TCGAutils, TEKRABber, TFBSTools, tidyCoverage, TnT, trackViewer, transcriptR, transmogR, tRNAscanImport, TVTB, txdbmaker, 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, crispRdesignR, driveR, ICAMS, locuszoomr, MAAPER, Signac, tepr Suggests Me AlphaMissenseR, AnnotationForge, AnnotationHub, annotatr, BSgenome, Chicago, DEXSeq, DFplyr, DiffBind, epialleleR, ExperimentHubData, fishpond, GenomicFeatures, GenomicRanges, GenomicTuples, ldblock, megadepth, methrix, Organism.dplyr, OUTRIDER, parglms, QDNAseq, RaggedExperiment, RAIDS, regioneReloaded, rtracklayer, scTreeViz, Seqinfo, sesame, splatter, SummarizedExperiment, systemPipeR, TFutils, UCSC.utils, VariantAnnotation, BioMartGOGeneSets, sesameData, xcoredata, seqpac, gkmSVM, GRIN2, polyRAD, Seurat Links To Me Build Report Build Report Package Archives

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

RetroSearch is an open source project built by @garambo | Open a GitHub Issue

Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo

HTML: 3.2 | Encoding: UTF-8 | Version: 0.7.4