Files in rtracklayer

R interface to genome annotation files and the UCSC genome browser

TODO

configure.ac

configure

NEWS

NAMESPACE

DESCRIPTION

INSTALL

LICENSE

build/vignette.rds

src/bigBed.h

src/readGFF.c

src/twoBit.c

src/bbiHelper.h

src/rtracklayer.h

src/Makevars.common

src/bigBed.c

src/Makevars.win

src/readGFF.h

src/twoBit.h

src/Makevars.in

src/bigWig.h

src/bigBedHelper.c

src/bigWig.c

src/utils.c

src/Makevars

src/S4Vectors_stubs.c

src/IRanges_stubs.c

src/bigBedHelper.h

src/XVector_stubs.c

src/handlers.c

src/R_init_rtracklayer.c

src/utils.h

src/bbiHelper.c

src/handlers.h

src/chain_io.c

src/ucsc/bigBed.h

src/ucsc/bwgInternal.h

src/ucsc/errCatch.h

src/ucsc/net.h

src/ucsc/https.c

src/ucsc/sqlList.h

src/ucsc/pipeline.c

src/ucsc/twoBit.c

src/ucsc/common.h

src/ucsc/aliType.c

src/ucsc/basicBed.c

src/ucsc/cirTree.h

src/ucsc/bbiRead.c

src/ucsc/cirTree.c

src/ucsc/net.c

src/ucsc/_portimpl.c

src/ucsc/htmlColor.h

src/ucsc/zlibFace.c

src/ucsc/wildcmp.c

src/ucsc/bigBed.c

src/ucsc/htmlColor.c

src/ucsc/_cheapcgi.c

src/ucsc/twoBit.h

src/ucsc/binRange.c

src/ucsc/asParse.c

src/ucsc/_portimpl.h

src/ucsc/rbTree.c

src/ucsc/bits.h

src/ucsc/memgfx.h

src/ucsc/zlibFace.h

src/ucsc/https.h

src/ucsc/dlist.h

src/ucsc/udc.c

src/ucsc/localmem.c

src/ucsc/memalloc.c

src/ucsc/bigWig.h

src/ucsc/portable.h

src/ucsc/bits.c

src/ucsc/options.h

src/ucsc/rangeTree.h

src/ucsc/basicBed.h

src/ucsc/localmem.h

src/ucsc/htmshell.h

src/ucsc/hash.c

src/ucsc/aliType.h

src/ucsc/bPlusTree.h

src/ucsc/tokenizer.h

src/ucsc/pipeline.h

src/ucsc/obscure.c

src/ucsc/bwgQuery.c

src/ucsc/base64.c

src/ucsc/errAbort.c

src/ucsc/cheapcgi.h

src/ucsc/dnaseq.h

src/ucsc/dnaseq.c

src/ucsc/dlist.c

src/ucsc/binRange.h

src/ucsc/hmmstats.h

src/ucsc/dystring.c

src/ucsc/memalloc.h

src/ucsc/common.c

src/ucsc/base64.h

src/ucsc/dnautil.c

src/ucsc/hash.h

src/ucsc/bwgCreate.c

src/ucsc/sqlList.c

src/ucsc/memgfx.c

src/ucsc/verbose.c

src/ucsc/oswin9x.c

src/ucsc/asParse.h

src/ucsc/dnautil.h

src/ucsc/verbose.h

src/ucsc/linefile.h

src/ucsc/dystring.h

src/ucsc/rangeTree.c

src/ucsc/osunix.c

src/ucsc/os.c

src/ucsc/obscure.h

src/ucsc/sig.h

src/ucsc/sqlNum.h

src/ucsc/rbTree.h

src/ucsc/portimpl.h

src/ucsc/linefile.c

src/ucsc/sqlNum.c

src/ucsc/bPlusTree.c

src/ucsc/internet.c

src/ucsc/udc.h

src/ucsc/bbiWrite.c

src/ucsc/tokenizer.c

src/ucsc/bbiFile.h

src/ucsc/internet.h

src/ucsc/errAbort.h

src/ucsc/hmmstats.c

data/targets.rda

data/cpneTrack.rda

R/bam.R R/ucsc.R R/twobit.R R/fasta.R R/chain.R R/quickload.R R/trackDb.R R/utils.R R/wig.R R/io.R R/bed.R R/compression.R R/ranges.R R/trackhub.R R/zzz.R R/igv.R R/web.R R/gff.R R/test_rtracklayer_package.R R/bigBed.R R/browser.R R/readGFF.R R/index.R R/bigWig.R R/tabix.R R/ncbi.R R/trackTable.R demo/targets.R

demo/00Index

vignettes/rtracklayer.Rnw

vignettes/example.bed

man/FastaFile-class.Rd man/TrackHub-class.Rd man/ucscTrackLine-class.Rd man/IntegerRangesList-methods.Rd man/laySequence-methods.Rd man/ucscSession-class.Rd man/GFFFile-class.Rd man/ucscView-class.Rd man/readGFF.Rd man/ucscTrackModes-class.Rd man/browseGenome.Rd man/browserViews-methods.Rd man/browserView-class.Rd man/cpneTrack.Rd man/BEDFile-class.Rd man/BigWigFile.Rd man/basicTrackLine-class.Rd man/QuickloadGenome-class.Rd man/GRangesForUCSCGenome.Rd man/liftOver.Rd man/Chain-class.Rd man/BigWigSelection-class.Rd man/BrowserViewList-class.Rd man/BigBedFile.Rd man/UCSCFile-class.Rd man/browserSession-methods.Rd man/BamFile-methods.Rd man/Bed15TrackLine-class.Rd man/TwoBitFile-class.Rd man/GenomicSelection.Rd man/RTLFile-class.Rd man/export.Rd man/wigTrackLine-class.Rd man/wigToBigWig.Rd man/TabixFile-methods.Rd man/ucscTrackModes-methods.Rd man/activeView-methods.Rd man/BigBedSelection.rd man/UCSCTableQuery-class.Rd man/TrackHubGenome-class.Rd man/tracks-methods.Rd man/browserView-methods.Rd man/Quickload-class.Rd man/targets.Rd man/GenomicData.Rd man/browserSession-class.Rd man/UCSCData-class.Rd man/layTrack-methods.Rd man/ucscGenomes.Rd man/TrackDb-class.Rd man/blocks-methods.Rd man/asBED.Rd man/genomeBrowsers.Rd man/WIGFile-class.Rd man/UCSCSchema-class.Rd man/asGFF.Rd tests/rtracklayer_unit_tests.R

inst/CITATION

inst/doc/rtracklayer.Rnw

inst/doc/rtracklayer.R inst/doc/rtracklayer.pdf

inst/extdata/demo.narrowPeak.gz

inst/notes/requirements.tex

inst/notes/design.org

inst/notes/use-cases.tex

inst/scripts/twobit.R inst/scripts/cpneTrack.R inst/unitTests/test_bw.R inst/unitTests/test_bed.R inst/unitTests/test_trackhub.R inst/unitTests/test_wig.R inst/unitTests/test_gff.R inst/unitTests/test_bb.R inst/unitTests/test_twoBit.R inst/unitTests/test_bedGraph.R inst/tests/test.R

inst/tests/test.gtf

inst/tests/test.bedGraph

inst/tests/test.2bit

inst/tests/test.bw

inst/tests/variableStep.wig

inst/tests/test.bed15

inst/tests/variableStep.bw

inst/tests/test.bedpe

inst/tests/test.bed

inst/tests/v3.gff

inst/tests/bed.wig

inst/tests/step.wig

inst/tests/v2.gff

inst/tests/test.bb

inst/tests/bed.bw

inst/tests/multi.wig

inst/tests/test.xmfa

inst/tests/v1.gff

inst/tests/gtf.gff

inst/tests/genes.gff3

inst/tests/trackhub/hub.txt

inst/tests/trackhub/genomes.txt

inst/tests/trackhub/hg19/wgEncodeUWDukeDnaseGM12878.fdr01peaks.hg19.bb

inst/tests/trackhub/hg19/trackDb.txt

inst/tests/quickload/contents.txt

inst/tests/quickload/T_species_Oct_2011/bedGraphData.bw

inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz

inst/tests/quickload/T_species_Oct_2011/bedData.bed.gz.tbi

inst/tests/quickload/T_species_Oct_2011/T_species_Oct_2011.2bit

inst/tests/quickload/T_species_Oct_2011/mod_chromInfo.txt

inst/tests/quickload/T_species_Oct_2011/annots.xml

rtracklayer documentation built on Nov. 8, 2020, 6:50 p.m.