This package is for version 3.6 of Bioconductor;
for the stable, up-to-date release version, see
rtracklayer.
R interface to genome annotation files and the UCSC genome browser
Bioconductor version: 3.6
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Maintainer: Michael Lawrence <michafla at gene.com>
Citation (from within R, enter citation("rtracklayer")):
Installation
To install this package, start R (version "3.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("rtracklayer")
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("rtracklayer")
Details
Version
1.38.3
In Bioconductor since
BioC 2.2 (R-2.7) (16 years)
License
Artistic-2.0 + file
LICENSE
Imports
XML (>= 1.98-0),
BiocGenerics(>= 0.13.8),
S4Vectors(>= 0.13.13),
IRanges(>= 2.11.12),
XVector(>= 0.9.4),
GenomeInfoDb(>= 1.3.14),
Biostrings(>= 2.43.7),
zlibbioc, RCurl (>= 1.4-2),
Rsamtools(>= 1.17.8),
GenomicAlignments(>= 1.5.4), tools
System Requirements
See More
Suggests
BSgenome(>= 1.33.4),
humanStemCell,
microRNA(>= 1.1.1),
genefilter,
limma,
org.Hs.eg.db,
hgu133plus2.db,
GenomicFeatures,
BSgenome.Hsapiens.UCSC.hg19,
TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit
Enhances
Depends On Me
BSgenome,
ChIPComp,
CoverageView,
cummeRbund,
EatonEtAlChIPseq,
exomePeak,
geneXtendeR,
GenomicFiles,
groHMM,
Guitar,
HelloRanges,
IdeoViz,
MethylSeekR,
r3Cseq,
regioneR,
RIPSeeker,
spliceR
Imports Me
AnnotationHubData,
annotatr,
ATACseqQC,
ballgown,
BiSeq,
branchpointer,
BSgenome,
CAGEr,
casper,
CexoR,
chipenrich,
chipenrich.data,
ChIPseeker,
ChromHeatMap,
chromswitch,
CNEr,
coMET,
CompGO,
consensusSeekeR,
contiBAIT,
conumee,
customProDB,
DeepBlueR,
derfinder,
diffloop,
DMCHMM,
ensembldb,
erma,
esATAC,
FourCSeq,
FunciSNP,
FunciSNP.data,
genbankr,
geneAttribution,
geneLenDataBase,
genomation,
GenomicFeatures,
GenomicInteractions,
genotypeeval,
ggbio,
GGtools,
gmapR,
GOTHiC,
gQTLBase,
GreyListChIP,
Gviz,
gwascat,
hiAnnotator,
HiTC,
HTSeqGenie,
IsoformSwitchAnalyzeR,
karyoploteR,
MADSEQ,
MEDIPS,
metagene,
methyAnalysis,
methylKit,
motifbreakR,
MotifDb,
NADfinder,
normr,
Pbase,
PGA,
proBAMr,
PureCN,
qsea,
QuasR,
RCAS,
recount,
recoup,
regioneR,
Repitools,
RiboProfiling,
RNAprobR,
roar,
seqplots,
SGSeq,
soGGi,
SVM2CRM,
TFBSTools,
trackViewer,
transcriptR,
TSRchitect,
VariantAnnotation,
VariantTools,
wavClusteR,
wiggleplotr
Suggests Me
alpine,
AnnotationHub,
BiocFileCache,
biovizBase,
ChIPpeakAnno,
CINdex,
compEpiTools,
CrispRVariants,
dsQTL,
ELMER,
epivizrData,
FDb.FANTOM4.promoters.hg19,
GenomicAlignments,
GenomicRanges,
GeuvadisTranscriptExpr,
goseq,
InPAS,
interactiveDisplay,
metaseqR,
methylumi,
miRBaseConverter,
MotIV,
MutationalPatterns,
NarrowPeaks,
oneChannelGUI,
OrganismDbi,
PasillaTranscriptExpr,
PICS,
PING,
pqsfinder,
R453Plus1Toolbox,
Ringo,
rMAT,
RnBeads,
RSVSim,
signeR,
similaRpeak,
triplex,
TSSi,
TVTB
Links To Me
Package Archives
Follow Installation instructions to use this package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/rtracklayer
Source Repository (Developer Access)
git clone git@git.bioconductor.org:packages/rtracklayer