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
Version1.34.2

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"

Functions

2BitFile Man page
2BitFile-class Man page
activeView Man page
activeView<- Man page
activeView,BrowserSession-method Man page
activeView<--methods Man page
activeView-methods Man page
activeView,UCSCView-method Man page
asBED Man page
asBED,GAlignments-method Man page
asBED,GRangesList-method Man page
asGFF Man page
asGFF,GRangesList-method Man page
BasicTrackLine-class Man page
BED15File Man page
BED15File-class Man page
Bed15TrackLine-class Man page
BEDFile Man page
BEDFile-class Man page
BEDGraphFile Man page
BEDGraphFile-class Man page
BEDPEFile Man page
BEDPEFile-class Man page
BigWigFile Man page
BigWigFile-class Man page
BigWigFileList Man page
BigWigFileList-class Man page
BigWigSelection Man page
BigWigSelection-class Man page
blocks Man page
blocks,GenomicRanges-method Man page
blocks-methods Man page
browseGenome Man page
browseGenome,GenomicRangesORGenomicRangesList-method Man page
browseGenome,missing-method Man page
browserSession Man page
browserSession<- Man page
browserSession,BrowserView-method Man page
browserSession,character-method Man page
BrowserSession-class Man page
browserSession-methods Man page
browserSession,missing-method Man page
browserSession,UCSCTableQuery-method Man page
browserSession<-,UCSCTableQuery,UCSCSession-method Man page
browserView Man page
BrowserView-class Man page
BrowserViewList Man page
BrowserViewList-class Man page
browserView-methods Man page
browserViews Man page
browserViews-methods Man page
browserViews,UCSCSession-method Man page
browserView,UCSCSession-method Man page
BWFile Man page
BWFile-class Man page
ChainBlock-class Man page
Chain-class Man page
ChainFile Man page
ChainFile-class Man page
chrom Man page
chrom<- Man page
chrom<-,GRanges-method Man page
chrom,GRanges-method Man page
chrom<-,RangesList-method Man page
chrom,RangesList-method Man page
class:2BitFile Man page
class:BED15File Man page
class:BEDFile Man page
class:BEDGraphFile Man page
class:BigWigFile Man page
class:BigWigFileList Man page
class:BWFile Man page
class:Chain Man page
class:ChainBlock Man page
class:ChainFile Man page
class:CompressedFile Man page
class:FastaFile Man page
class:GFF1File Man page
class:GFF2File Man page
class:GFF3File Man page
class:GFFFile Man page
class:GTFFile Man page
class:GVFFile Man page
class:Quickload Man page
class:QuickloadGenome Man page
class:RTLFile Man page
class:TrackDb Man page
class:TwoBitFile Man page
class:UCSCFile Man page
class:WIGFile Man page
coerce,BasicTrackLine,character-method Man page
coerce,BasicTrackLine,GraphTrackLine-method Man page
coerce,Bed15TrackLine,character-method Man page
coerce,character,BasicTrackLine-method Man page
coerce,character,Bed15TrackLine-method Man page
coerce,character,GraphTrackLine-method Man page
coerce,character,Quickload-method Man page
coerce,character,TrackLine-method Man page
coerce,GenomicRanges,BigWigSelection-method Man page
coerce,GRanges,UCSCData-method Man page
coerce,GraphTrackLine,BasicTrackLine-method Man page
coerce,GraphTrackLine,character-method Man page
coerce,RangesList,BigWigSelection-method Man page
coerce,TrackLine,character-method Man page
coerce,UCSCData,GRanges-method Man page
CompressedFile-class Man page
cpneTrack Man page
export Man page
export.2bit Man page
export.2bit,ANY-method Man page
export,ANY,BamFile,ANY-method Man page
export,ANY,BEDFile,ANY-method Man page
export,ANY,BigWigFile,ANY-method Man page
export,ANY,character,character-method Man page
export,ANY,character,missing-method Man page
export,ANY,CompressedFile,missing-method Man page
export,ANY,connection,character-method Man page
export,ANY,connection,missing-method Man page
export,ANY,FastaFile,ANY-method Man page
export,ANY,GFFFile,ANY-method Man page
export,ANY,missing,character-method Man page
export,ANY,TabSeparatedFile,ANY-method Man page
export,ANY,TwoBitFile,ANY-method Man page
export,ANY,UCSCFile,ANY-method Man page
export,ANY,WIGFile,ANY-method Man page
export.bed Man page
export.bed15 Man page
export.bed15,ANY-method Man page
export.bed15,UCSCData-method Man page
export.bed,ANY-method Man page
export.bedGraph Man page
export.bedGraph,ANY-method Man page
export.bed,UCSCData,characterORconnection-method Man page
export.bw Man page
export.bw,ANY-method Man page
export,DNAStringSet,character,ANY-method Man page
export,DNAStringSet,TwoBitFile,ANY-method Man page
export,GAlignmentPairs,BamFile,ANY-method Man page
export,GAlignments,BamFile,ANY-method Man page
export,GenomicRanges,BED15File,ANY-method Man page
export,GenomicRanges,BEDFile,ANY-method Man page
export,GenomicRanges,BigWigFile,ANY-method Man page
export,GenomicRanges,GFFFile,ANY-method Man page
export,GenomicRangesList,BEDFile,ANY-method Man page
export,GenomicRangesList,GFFFile,ANY-method Man page
export,GenomicRangesList,UCSCFile,ANY-method Man page
export,GenomicRangesList,WIGFile,ANY-method Man page
export,GenomicRanges,TabSeparatedFile,ANY-method Man page
export,GenomicRanges,UCSCFile,ANY-method Man page
export,GenomicRanges,WIGFile,ANY-method Man page
export.gff Man page
export.gff1 Man page
export.gff1,ANY-method Man page
export.gff2 Man page
export.gff2,ANY-method Man page
export.gff3 Man page
export.gff3,ANY-method Man page
export.gff,ANY-method Man page
export.gff,UCSCData,characterORconnection-method Man page
export,GRangesList,BEDFile,ANY-method Man page
export,GRangesList,GFFFile,ANY-method Man page
export,List,BigWigFile,ANY-method Man page
exportToTabix Man page
exportToTabix,ANY,character-method Man page
export.ucsc Man page
export.ucsc,ANY,ANY-method Man page
export.ucsc,ANY,RTLFile-method Man page
export,UCSCData,BEDFile,ANY-method Man page
export,UCSCData,UCSCFile,ANY-method Man page
export,UCSCData,WIGFile,ANY-method Man page
export.ucsc,UCSCData,characterORconnection-method Man page
export.wig Man page
export.wig,ANY-method Man page
export,XStringSet,FastaFile,ANY-method Man page
FastaFile Man page
FastaFile-class Man page
FileForFormat Man page
formatDescription Man page
formatDescription,UCSCSchema-method Man page
genomeBrowsers Man page
genome<-,BrowserSession-method Man page
genome,BrowserSession-method Man page
genome,GFFFile-method Man page
genome,QuickloadGenome-method Man page
genome,Quickload-method Man page
genome,ucscCart-method Man page
genome,UCSCSchema-method Man page
genome,UCSCSchema-method Man page
genome<-,UCSCSession-method Man page
genome,UCSCSession-method Man page
GenomicData Man page
GenomicRangesORGenomicRangesList-class Man page
GenomicSelection Man page
getSeq,TwoBitFile-method Man page
getTable Man page
getTable,UCSCSession-method Man page
getTable,UCSCTableQuery-method Man page
GFF1File Man page
GFF1File-class Man page
GFF2File Man page
GFF2File-class Man page
GFF3File Man page
GFF3File-class Man page
GFFcolnames Man page
GFFFile Man page
GFFFile-class Man page
GRangesForBSGenome Man page
GRangesForUCSCGenome Man page
GraphTrackLine-class Man page
GTFFile Man page
GTFFile-class Man page
GVFFile Man page
GVFFile-class Man page
import Man page
import.2bit Man page
import.2bit,ANY-method Man page
import,BamFile,ANY,ANY-method Man page
import.bed Man page
import.bed15 Man page
import.bed15,ANY-method Man page
import,BED15File,ANY,ANY-method Man page
import.bed,ANY-method Man page
import,BEDFile,ANY,ANY-method Man page
import.bedGraph Man page
import.bedGraph,ANY-method Man page
import,BEDPEFile,ANY,ANY-method Man page
import,BigWigFile,ANY,ANY-method Man page
import.bw Man page
import.bw,ANY-method Man page
import.chain Man page
import.chain,ANY-method Man page
import,ChainFile,ANY,ANY-method Man page
import,character,character,ANY-method Man page
import,character,missing,ANY-method Man page
import,CompressedFile,missing,ANY-method Man page
import,connection,character,ANY-method Man page
import,connection,missing,ANY-method Man page
import,FastaFile,ANY,ANY-method Man page
import.gff Man page
import.gff1 Man page
import.gff1,ANY-method Man page
import.gff2 Man page
import.gff2,ANY-method Man page
import.gff3 Man page
import.gff3,ANY-method Man page
import.gff,ANY-method Man page
import,GFFFile,ANY,ANY-method Man page
import,missing,ANY,character-method Man page
import,TabixFile,ANY,ANY-method Man page
import,TwoBitFile,ANY,ANY-method Man page
import.ucsc Man page
import.ucsc,ANY-method Man page
import,UCSCFile,ANY,ANY-method Man page
import.ucsc,RTLFile-method Man page
import.wig Man page
import.wig,ANY-method Man page
import,WIGFile,ANY,ANY-method Man page
initialize,UCSCData-method Man page
initialize,UCSCSession-method Man page
length,QuickloadGenome-method Man page
length,Quickload-method Man page
liftOver Man page
liftOver,GenomicRanges,Chain-method Man page
mcols,QuickloadGenome-method Man page
names,BrowserSession-method Man page
names,QuickloadGenome-method Man page
names<-,UCSCTableQuery-method Man page
names,UCSCTableQuery-method Man page
nrow,UCSCSchema-method Man page
offset,ChainBlock-method Man page
organism,QuickloadGenome-method Man page
path Man page
path,BigWigFileList-method Man page
path,RTLFile-method Man page
quickload Man page
Quickload Man page
[[,Quickload,ANY,ANY-method Man page
Quickload-class Man page
QuickloadGenome Man page
QuickloadGenome-class Man page
$,Quickload-method Man page
range<- Man page
range,BrowserSession-method Man page
ranges,ChainBlock-method Man page
RangesList-methods Man page
range,ucscCart-method Man page
range<-,UCSCSession-method Man page
range,UCSCSession-method Man page
range<-,UCSCTableQuery-method Man page
range,UCSCTableQuery-method Man page
range<-,UCSCView-method Man page
range,UCSCView-method Man page
readGFF Man page
referenceSequence Man page
referenceSequence<- Man page
referenceSequence<-,QuickloadGenome-method Man page
referenceSequence,QuickloadGenome-method Man page
releaseDate,QuickloadGenome-method Man page
resource Man page
reversed Man page
reversed,ChainBlock-method Man page
RTLFile-class Man page
score,ANY-method Man page
score,ChainBlock-method Man page
score,GenomicRangesORGRangesList-method Man page
seqinfo,BigWigFile-method Man page
seqinfo,DNAStringSet-method Man page
SeqinfoForBSGenome Man page
SeqinfoForUCSCGenome Man page
seqinfo<-,QuickloadGenome-method Man page
seqinfo,QuickloadGenome-method Man page
seqinfo,TwoBitFile-method Man page
seqinfo,UCSCSession-method Man page
sequence<- Man page
sequence<--methods Man page
show,BrowserSession-method Man page
show,BrowserView-method Man page
show,QuickloadGenome-method Man page
show,Quickload-method Man page
show,RTLFile-method Man page
show,TrackLine-method Man page
show,UCSCData-method Man page
show,UCSCTableQuery-method Man page
space,ChainBlock-method Man page
split,UCSCData,ANY-method Man page
split,UCSCData,Vector-method Man page
summary,BigWigFile-method Man page
tableName Man page
tableName<- Man page
tableNames Man page
tableNames,UCSCTableQuery-method Man page
tableName,UCSCSchema-method Man page
tableName<-,UCSCTableQuery-method Man page
tableName,UCSCTableQuery-method Man page
targets Man page
track Man page
track<- Man page
track<-,BrowserSession,ANY-method Man page
[[<-,TrackDb,ANY,ANY-method Man page
[[,TrackDb,ANY,ANY-method Man page
TrackDb-class Man page
$<-,TrackDb-method Man page
$,TrackDb-method Man page
TrackLine-class Man page
track<--methods Man page
trackName Man page
trackName<- Man page
trackNames Man page
trackNames<- Man page
trackNames,BrowserSession-method Man page
trackNames<--methods Man page
trackNames-methods Man page
trackNames,UCSCSession-method Man page
trackNames,UCSCTableQuery-method Man page
trackNames<-,UCSCTrackModes-method Man page
trackNames,UCSCTrackModes-method Man page
trackNames<-,UCSCView-method Man page
trackNames,UCSCView-method Man page
trackName<-,UCSCTableQuery-method Man page
trackName,UCSCTableQuery-method Man page
track<-,QuickloadGenome,ANY-method Man page
track<-,QuickloadGenome,character-method Man page
track,QuickloadGenome-method Man page
track<-,QuickloadGenome,RsamtoolsFile-method Man page
track<-,QuickloadGenome,RTLFile-method Man page
track<-,TrackDb,ANY-method Man page
track<-,UCSCSession,GenomicRangesList-method Man page
track,UCSCSession-method Man page
track<-,UCSCSession,RTLFile-method Man page
track,UCSCTableQuery-method Man page
TwoBitFile Man page
TwoBitFile-class Man page
UCSCData-class Man page
UCSCFile Man page
UCSCFile-class Man page
ucscGenomes Man page
ucscSchema Man page
UCSCSchema-class Man page
ucscSchema,UCSCSchemaDescription-method Man page
ucscSchema,UCSCTableQuery-method Man page
UCSCSession-class Man page
ucscTableQuery Man page
UCSCTableQuery-class Man page
ucscTableQuery,UCSCSession-method Man page
ucscTrackModes Man page
ucscTrackModes<- Man page
[<-,UCSCTrackModes,ANY,ANY,ANY-method Man page
[,UCSCTrackModes,ANY,ANY-method Man page
ucscTrackModes,character-method Man page
UCSCTrackModes-class Man page
ucscTrackModes<--methods Man page
ucscTrackModes-methods Man page
ucscTrackModes,missing-method Man page
ucscTrackModes,UCSCSession-method Man page
ucscTrackModes,ucscTracks-method Man page
ucscTrackModes<-,UCSCView,character-method Man page
ucscTrackModes,UCSCView-method Man page
ucscTrackModes<-,UCSCView,UCSCTrackModes-method Man page
UCSCView-class Man page
uri Man page
uri,QuickloadGenome-method Man page
visible Man page
visible<- Man page
visible<-,BrowserView-method Man page
visible,BrowserView-method Man page
visible<-,UCSCView-method Man page
visible,UCSCView-method Man page
WIGFile Man page
WIGFile-class Man page
wigToBigWig Man page

Files

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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Please suggest features or report bugs with the GitHub issue tracker.

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