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.

AuthorMichael Lawrence, Vince Carey, Robert Gentleman
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0 + file LICENSE
Version1.34.1

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

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