rtracklayer: R interface to genome browsers and their annotation tracks

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
Date of publication
None
Maintainer
Michael Lawrence <michafla@gene.com>
License
Artistic-2.0 + file LICENSE
Version
1.34.1

View on Bioconductor

Man pages

activeView-methods
Accessing the active view
asBED
Coerce to BED structure
asGFF
Coerce to GFF structure
BamFile-methods
Export to BAM Files
basicTrackLine-class
Class "BasicTrackLine"
Bed15TrackLine-class
Class "Bed15TrackLine"
BEDFile-class
BEDFile objects
BigWigFile
BigWig Import and Export
BigWigSelection-class
Selection of ranges and columns
blocks-methods
Get blocks/exons
browseGenome
Browse a genome
browserSession-class
Class "BrowserSession"
browserSession-methods
Get a genome browser session
browserView-class
Class "BrowserView"
BrowserViewList-class
Lists of BrowserView
browserView-methods
Getting browser views
browserViews-methods
Getting the browser views
Chain-class
Chain objects
cpneTrack
CPNE1 SNP track
export
Import and export
FastaFile-class
FastaFile objects
genomeBrowsers
Get available genome browsers
GenomicData
Data on a Genome
GenomicSelection
Genomic data selection
GFFFile-class
GFFFile objects
GRangesForUCSCGenome
GRanges for a Genome
laySequence-methods
Load a sequence
layTrack-methods
Laying tracks
liftOver
Lift intervals between genome builds
Quickload-class
Quickload Access
QuickloadGenome-class
Quickload Genome Access
RangesList-methods
Ranges on a Genome
readGFF
Reads a file in GFF format
RTLFile-class
RTLFile objects
TabixFile-methods
TabixFile Import/Export
targets
microRNA target sites
TrackDb-class
Track Databases
tracks-methods
Accessing track names
TwoBitFile-class
2bit Files
UCSCData-class
Class "UCSCData"
UCSCFile-class
UCSCFile objects
ucscGenomes
Get available genomes on UCSC
UCSCSchema-class
UCSC Schema
ucscSession-class
Class "UCSCSession"
UCSCTableQuery-class
Querying UCSC Tables
ucscTrackLine-class
Class "TrackLine"
ucscTrackModes-class
Class "UCSCTrackModes"
ucscTrackModes-methods
Accessing UCSC track modes
ucscView-class
Class "UCSCView"
WIGFile-class
WIG Import and Export
wigToBigWig
Convert WIG to BigWig
wigTrackLine-class
Class "GraphTrackLine"

Files in this package

rtracklayer/DESCRIPTION
rtracklayer/LICENSE
rtracklayer/NAMESPACE
rtracklayer/NEWS
rtracklayer/R
rtracklayer/R/bam.R
rtracklayer/R/bed.R
rtracklayer/R/bigWig.R
rtracklayer/R/browser.R
rtracklayer/R/chain.R
rtracklayer/R/compression.R
rtracklayer/R/fasta.R
rtracklayer/R/gff.R
rtracklayer/R/index.R
rtracklayer/R/io.R
rtracklayer/R/ncbi.R
rtracklayer/R/quickload.R
rtracklayer/R/ranges.R
rtracklayer/R/readGFF.R
rtracklayer/R/tabix.R
rtracklayer/R/test_rtracklayer_package.R
rtracklayer/R/trackDb.R
rtracklayer/R/trackTable.R
rtracklayer/R/twobit.R
rtracklayer/R/ucsc.R
rtracklayer/R/utils.R
rtracklayer/R/web.R
rtracklayer/R/wig.R
rtracklayer/R/zzz.R
rtracklayer/TODO
rtracklayer/build
rtracklayer/build/vignette.rds
rtracklayer/configure
rtracklayer/configure.ac
rtracklayer/data
rtracklayer/data/cpneTrack.rda
rtracklayer/data/targets.rda
rtracklayer/demo
rtracklayer/demo/00Index
rtracklayer/demo/targets.R
rtracklayer/inst
rtracklayer/inst/CITATION
rtracklayer/inst/doc
rtracklayer/inst/doc/rtracklayer.R
rtracklayer/inst/doc/rtracklayer.Rnw
rtracklayer/inst/doc/rtracklayer.pdf
rtracklayer/inst/extdata
rtracklayer/inst/extdata/demo.narrowPeak.gz
rtracklayer/inst/notes
rtracklayer/inst/notes/design.org
rtracklayer/inst/notes/requirements.tex
rtracklayer/inst/notes/use-cases.tex
rtracklayer/inst/scripts
rtracklayer/inst/scripts/cpneTrack.R
rtracklayer/inst/scripts/twobit.R
rtracklayer/inst/tests
rtracklayer/inst/tests/bed.bw
rtracklayer/inst/tests/bed.wig
rtracklayer/inst/tests/genes.gff3
rtracklayer/inst/tests/gtf.gff
rtracklayer/inst/tests/multi.wig
rtracklayer/inst/tests/quickload
rtracklayer/inst/tests/quickload/T_species_Oct_2011
rtracklayer/inst/tests/quickload/T_species_Oct_2011/T_species_Oct_2011.2bit
rtracklayer/inst/tests/quickload/T_species_Oct_2011/annots.xml
rtracklayer/inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz
rtracklayer/inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz.tbi
rtracklayer/inst/tests/quickload/T_species_Oct_2011/bedGraphData.bw
rtracklayer/inst/tests/quickload/T_species_Oct_2011/mod_chromInfo.txt
rtracklayer/inst/tests/quickload/contents.txt
rtracklayer/inst/tests/step.wig
rtracklayer/inst/tests/test.2bit
rtracklayer/inst/tests/test.R
rtracklayer/inst/tests/test.bed
rtracklayer/inst/tests/test.bed15
rtracklayer/inst/tests/test.bedGraph
rtracklayer/inst/tests/test.bedpe
rtracklayer/inst/tests/test.bw
rtracklayer/inst/tests/test.gtf
rtracklayer/inst/tests/v1.gff
rtracklayer/inst/tests/v2.gff
rtracklayer/inst/tests/v3.gff
rtracklayer/inst/tests/variableStep.bw
rtracklayer/inst/tests/variableStep.wig
rtracklayer/inst/unitTests
rtracklayer/inst/unitTests/test_bed.R
rtracklayer/inst/unitTests/test_bedGraph.R
rtracklayer/inst/unitTests/test_bw.R
rtracklayer/inst/unitTests/test_gff.R
rtracklayer/inst/unitTests/test_twoBit.R
rtracklayer/inst/unitTests/test_wig.R
rtracklayer/load.R
rtracklayer/man
rtracklayer/man/BEDFile-class.Rd
rtracklayer/man/BamFile-methods.Rd
rtracklayer/man/Bed15TrackLine-class.Rd
rtracklayer/man/BigWigFile.Rd
rtracklayer/man/BigWigSelection-class.Rd
rtracklayer/man/BrowserViewList-class.Rd
rtracklayer/man/Chain-class.Rd
rtracklayer/man/FastaFile-class.Rd
rtracklayer/man/GFFFile-class.Rd
rtracklayer/man/GRangesForUCSCGenome.Rd
rtracklayer/man/GenomicData.Rd
rtracklayer/man/GenomicSelection.Rd
rtracklayer/man/Quickload-class.Rd
rtracklayer/man/QuickloadGenome-class.Rd
rtracklayer/man/RTLFile-class.Rd
rtracklayer/man/RangesList-methods.Rd
rtracklayer/man/TabixFile-methods.Rd
rtracklayer/man/TrackDb-class.Rd
rtracklayer/man/TwoBitFile-class.Rd
rtracklayer/man/UCSCData-class.Rd
rtracklayer/man/UCSCFile-class.Rd
rtracklayer/man/UCSCSchema-class.Rd
rtracklayer/man/UCSCTableQuery-class.Rd
rtracklayer/man/WIGFile-class.Rd
rtracklayer/man/activeView-methods.Rd
rtracklayer/man/asBED.Rd
rtracklayer/man/asGFF.Rd
rtracklayer/man/basicTrackLine-class.Rd
rtracklayer/man/blocks-methods.Rd
rtracklayer/man/browseGenome.Rd
rtracklayer/man/browserSession-class.Rd
rtracklayer/man/browserSession-methods.Rd
rtracklayer/man/browserView-class.Rd
rtracklayer/man/browserView-methods.Rd
rtracklayer/man/browserViews-methods.Rd
rtracklayer/man/cpneTrack.Rd
rtracklayer/man/export.Rd
rtracklayer/man/genomeBrowsers.Rd
rtracklayer/man/laySequence-methods.Rd
rtracklayer/man/layTrack-methods.Rd
rtracklayer/man/liftOver.Rd
rtracklayer/man/readGFF.Rd
rtracklayer/man/targets.Rd
rtracklayer/man/tracks-methods.Rd
rtracklayer/man/ucscGenomes.Rd
rtracklayer/man/ucscSession-class.Rd
rtracklayer/man/ucscTrackLine-class.Rd
rtracklayer/man/ucscTrackModes-class.Rd
rtracklayer/man/ucscTrackModes-methods.Rd
rtracklayer/man/ucscView-class.Rd
rtracklayer/man/wigToBigWig.Rd
rtracklayer/man/wigTrackLine-class.Rd
rtracklayer/src
rtracklayer/src/IRanges_stubs.c
rtracklayer/src/Makevars
rtracklayer/src/Makevars.common
rtracklayer/src/Makevars.in
rtracklayer/src/Makevars.win
rtracklayer/src/R_init_rtracklayer.c
rtracklayer/src/S4Vectors_stubs.c
rtracklayer/src/XVector_stubs.c
rtracklayer/src/bigWig.c
rtracklayer/src/bigWig.h
rtracklayer/src/chain_io.c
rtracklayer/src/handlers.c
rtracklayer/src/handlers.h
rtracklayer/src/readGFF.c
rtracklayer/src/readGFF.h
rtracklayer/src/rtracklayer.h
rtracklayer/src/twoBit.c
rtracklayer/src/twoBit.h
rtracklayer/src/ucsc
rtracklayer/src/ucsc/_cheapcgi.c
rtracklayer/src/ucsc/_portimpl.c
rtracklayer/src/ucsc/_portimpl.h
rtracklayer/src/ucsc/bPlusTree.c
rtracklayer/src/ucsc/bPlusTree.h
rtracklayer/src/ucsc/base64.c
rtracklayer/src/ucsc/base64.h
rtracklayer/src/ucsc/bbiFile.h
rtracklayer/src/ucsc/bbiRead.c
rtracklayer/src/ucsc/bbiWrite.c
rtracklayer/src/ucsc/bigBed.h
rtracklayer/src/ucsc/bigWig.h
rtracklayer/src/ucsc/bits.c
rtracklayer/src/ucsc/bits.h
rtracklayer/src/ucsc/bwgCreate.c
rtracklayer/src/ucsc/bwgInternal.h
rtracklayer/src/ucsc/bwgQuery.c
rtracklayer/src/ucsc/cheapcgi.h
rtracklayer/src/ucsc/cirTree.c
rtracklayer/src/ucsc/cirTree.h
rtracklayer/src/ucsc/common.c
rtracklayer/src/ucsc/common.h
rtracklayer/src/ucsc/dlist.c
rtracklayer/src/ucsc/dlist.h
rtracklayer/src/ucsc/dnaseq.c
rtracklayer/src/ucsc/dnaseq.h
rtracklayer/src/ucsc/dnautil.c
rtracklayer/src/ucsc/dnautil.h
rtracklayer/src/ucsc/dystring.c
rtracklayer/src/ucsc/dystring.h
rtracklayer/src/ucsc/errAbort.c
rtracklayer/src/ucsc/errAbort.h
rtracklayer/src/ucsc/errCatch.h
rtracklayer/src/ucsc/hash.c
rtracklayer/src/ucsc/hash.h
rtracklayer/src/ucsc/hmmstats.c
rtracklayer/src/ucsc/hmmstats.h
rtracklayer/src/ucsc/htmshell.h
rtracklayer/src/ucsc/https.c
rtracklayer/src/ucsc/https.h
rtracklayer/src/ucsc/internet.c
rtracklayer/src/ucsc/internet.h
rtracklayer/src/ucsc/linefile.c
rtracklayer/src/ucsc/linefile.h
rtracklayer/src/ucsc/localmem.c
rtracklayer/src/ucsc/localmem.h
rtracklayer/src/ucsc/memalloc.c
rtracklayer/src/ucsc/memalloc.h
rtracklayer/src/ucsc/net.c
rtracklayer/src/ucsc/net.h
rtracklayer/src/ucsc/obscure.c
rtracklayer/src/ucsc/obscure.h
rtracklayer/src/ucsc/options.h
rtracklayer/src/ucsc/os.c
rtracklayer/src/ucsc/osunix.c
rtracklayer/src/ucsc/oswin9x.c
rtracklayer/src/ucsc/pipeline.c
rtracklayer/src/ucsc/pipeline.h
rtracklayer/src/ucsc/portable.h
rtracklayer/src/ucsc/portimpl.h
rtracklayer/src/ucsc/rangeTree.c
rtracklayer/src/ucsc/rangeTree.h
rtracklayer/src/ucsc/rbTree.c
rtracklayer/src/ucsc/rbTree.h
rtracklayer/src/ucsc/sig.h
rtracklayer/src/ucsc/sqlNum.c
rtracklayer/src/ucsc/sqlNum.h
rtracklayer/src/ucsc/twoBit.c
rtracklayer/src/ucsc/twoBit.h
rtracklayer/src/ucsc/udc.c
rtracklayer/src/ucsc/udc.h
rtracklayer/src/ucsc/verbose.c
rtracklayer/src/ucsc/verbose.h
rtracklayer/src/ucsc/wildcmp.c
rtracklayer/src/ucsc/zlibFace.c
rtracklayer/src/ucsc/zlibFace.h
rtracklayer/src/utils.c
rtracklayer/src/utils.h
rtracklayer/tests
rtracklayer/tests/rtracklayer_unit_tests.R
rtracklayer/vignettes
rtracklayer/vignettes/example.bed
rtracklayer/vignettes/rtracklayer.Rnw