TxDb.Hsapiens.UCSC.hg19.knownGene

This is the released version of TxDb.Hsapiens.UCSC.hg19.knownGene; for the devel version, see TxDb.Hsapiens.UCSC.hg19.knownGene.

Annotation package for TxDb object(s)

Bioconductor version: Release (3.23)

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects

Author: Bioconductor Core Team, Bioconductor Package Maintainer <maintainer at bioconductor.org> [cre]

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

Citation (from within R, enter citation("TxDb.Hsapiens.UCSC.hg19.knownGene")):

Seminal Bioconductor project articles:

Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.

Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.

Installation

To install this package, start R (version "4.6") and enter:


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

BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	AnnotationData, Genetics, Homo_sapiens, TxDb
Version	3.22.1
License	Artistic-2.0
Depends	GenomicFeatures
Imports	AnnotationDbi
System Requirements
URL

Suggests
Linking To
Enhances
Depends On Me	FDb.InfiniumMethylation.hg19, Homo.sapiens, annotation, variants
Imports Me	appreci8R, ChIPQC, ChIPseeker, crupR, decompTumor2Sig, epimutacions, fourSynergy, HiLDA, musicatk, nearBynding, OutSplice, RareVariantVis, rGREAT, signifinder, uncoverappLib
Suggests Me	AllelicImbalance, AnnotationDbi, annotatr, ATACseqQC, beadarray, Bioc.gff, BiocParallel, biomvRCNS, biovizBase, borealis, bumphunter, ChIPpeakAnno, chromPlot, CNVRanger, cpvSNP, CRISPRseek, derfinder, derfinderPlot, dmrseq, EpiCompare, EpiMix, esATAC, FRASER, GA4GHclient, GA4GHshiny, gage, geneAttribution, GENESIS, GenomicAlignments, GenomicFeatures, GenomicInteractionNodes, GenVisR, geomeTriD, ggbio, gmapR, GOaGO, GRaNIE, groHMM, GUIDEseq, gwascat, HelloRanges, karyoploteR, MAST, MesKit, MutationalPatterns, NanoMethViz, OUTRIDER, pageRank, plotgardener, ProteoDisco, PureCN, R3CPET, ramr, regionalpcs, regionReport, rtracklayer, SGSeq, SOMNiBUS, StructuralVariantAnnotation, SummarizedExperiment, svaNUMT, svaRetro, TCGAutils, TFEA.ChIP, trackViewer, transcriptR, tximport, UMI4Cats, VariantAnnotation, VariantFiltering, VariantTools, chipenrich.data, cinaR, driveR, oncoPredict, SNPassoc
Links To Me

Package Archives

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

Source Package	TxDb.Hsapiens.UCSC.hg19.knownGene_3.22.1.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Package Short Url	https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/
Package Downloads Report	Download Stats