Package: rtracklayer 1.67.0

Michael Lawrence

rtracklayer: R interface to genome annotation files and the UCSC genome browser

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.

Authors:Michael Lawrence, Vince Carey, Robert Gentleman

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rtracklayer.pdf |rtracklayer.html✨
rtracklayer/json (API)
NEWS

# Install 'rtracklayer' in R:
install.packages('rtracklayer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • zlib– Compression library
  • openssl– Secure Sockets Layer toolkit
  • curl– Easy-to-use client-side URL transfer library
Datasets:

On BioConductor:rtracklayer-1.67.0(bioc 3.21)rtracklayer-1.66.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

annotationvisualizationdataimportzlibopensslcurl

12.62 score 483 packages 6.8k scripts 43k downloads 107 mentions 164 exports 49 dependencies

Last updated 1 months agofrom:1ab3e9222e. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 06 2024
R-4.5-win-x86_64WARNINGDec 06 2024
R-4.5-linux-x86_64WARNINGDec 06 2024
R-4.4-win-x86_64WARNINGDec 06 2024
R-4.4-mac-x86_64WARNINGDec 06 2024
R-4.4-mac-aarch64WARNINGDec 06 2024
R-4.3-win-x86_64WARNINGDec 06 2024
R-4.3-mac-x86_64WARNINGDec 06 2024
R-4.3-mac-aarch64WARNINGDec 06 2024

Exports:activeViewactiveView<-as.data.frameasBEDasGFFBED15FileBEDFileBEDGraphFileBEDPEFileBigBedFileBigBedSelectionBigWigFileBigWigFileListBigWigSelectionblocksbrowseGenomebrowserSessionbrowserSession<-browserViewbrowserViewsChainFilechromchrom<-cleanupBigBedCachecleanupBigWigCacheclosecoercedescriptionUrldescriptionUrl<-emailemail<-endend<-exportexport.2bitexport.bbexport.bedexport.bed15export.bedGraphexport.bwexport.gffexport.gff1export.gff2export.gff3export.ucscexport.wigexportToTabixFastaFileFileForFormatfileFormatgenomeGenomegenome<-genomeBrowsersgenomeFieldgenomeField<-genomeInfogenomeInfo<-genomesFilegenomesFile<-GenomicDataGenomicSelectiongetSeqgetTablegetTracksGFF1FileGFF2FileGFF3FileGFFcolnamesGFFFileGRangesForBSGenomeGRangesForUCSCGenomeGTFFileGVFFilehubhub<-hubUrlhubUrl<-importimport.2bitimport.bbimport.bedimport.bed15import.bedGraphimport.bwimport.chainimport.gffimport.gff1import.gff2import.gff3import.ucscimport.wiginitializeliftOverlongLabellongLabel<-mcolsnrowoffsetorganismpathquickloadQuickloadQuickloadGenomerange<-rangesreadGFFreadGFFAsGRangesreadGFFPragmasreferenceSequencereferenceSequence<-releaseDateresourcereversedscorescore<-seqinfoseqinfo<-SeqinfoForBSGenomeSeqinfoForUCSCGenomeshortLabelshortLabel<-showsniffGFFVersionspacesplitstartstart<-strandsummarytableNametableName<-tableNamestrackTracktrack<-TrackContainertrackFieldtrackField<-trackhubTrackHubTrackHubGenometrackNametrackName<-trackNamestrackNames<-TwoBitFileUCSCFileucscGenomesucscSchemaucscTableQueryucscTablesucscTrackModesucscTrackModes<-urivaluesviewURLvisiblevisible<-widthwidth<-WIGFilewigToBigWigwriteTrackHub

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArrayformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangeshttrIRangesjsonlitelambda.rlatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6RCurlrestfulrRhtslibrjsonRsamtoolsS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsXMLXVectoryamlzlibbioc

rtracklayer

Rendered fromrtracklayer.Rnwusingutils::Sweaveon Dec 06 2024.

Last update: 2023-10-20
Started: 2013-10-18

Readme and manuals

Help Manual

Help pageTopics
Accessing the active viewactiveView activeView,BrowserSession-method activeView,UCSCView-method activeView-methods activeView<- activeView<--methods
Coerce to BED structureasBED asBED,GAlignments-method asBED,GRangesList-method
Coerce to GFF structureasGFF asGFF,GRangesList-method
Export to BAM Filesexport,ANY,BamFile,ANY-method export,GAlignmentPairs,BamFile,ANY-method export,GAlignments,BamFile,ANY-method import,BamFile,ANY,ANY-method
Class "BasicTrackLine"BasicTrackLine-class coerce,BasicTrackLine,character-method coerce,character,BasicTrackLine-method
Class "Bed15TrackLine"Bed15TrackLine-class coerce,Bed15TrackLine,character-method coerce,character,Bed15TrackLine-method
BEDFile objectsBED15File BED15File-class BEDFile BEDFile-class BEDGraphFile BEDGraphFile-class BEDPEFile BEDPEFile-class BroadPeakFile BroadPeakFile-class class:BED15File class:BEDFile class:BEDGraphFile class:BroadPeakFile class:NarrowPeakFile export,ANY,BEDFile,ANY-method export,ANY,BEDPEFile,ANY-method export,GenomicRanges,BED15File,ANY-method export,GenomicRanges,BEDFile,ANY-method export,GenomicRangesList,BEDFile,ANY-method export,GRangesList,BEDFile,ANY-method export,Pairs,BEDPEFile,ANY-method export,UCSCData,BED15File,ANY-method export,UCSCData,BEDFile,ANY-method export.bed export.bed,ANY-method export.bed15 export.bed15,ANY-method export.bedGraph export.bedGraph,ANY-method import,BED15File,ANY,ANY-method import,BEDFile,ANY,ANY-method import,BEDPEFile,ANY,ANY-method import,BroadPeakFile,ANY,ANY-method import,BroadPeakFile,ANY-method import,NarrowPeakFile,ANY,ANY-method import,NarrowPeakFile,ANY-method import.bed import.bed,ANY-method import.bed15 import.bed15,ANY-method import.bedGraph import.bedGraph,ANY-method import.BroadPeak import.BroadPeak,ANY-method import.NarrowPeak import.NarrowPeak,ANY-method NarrowPeakFile NarrowPeakFile-class
BigBed Import and ExportBBFile BBFile-class BigBedFile BigBedFile-class class:BBFile class:BigBedFile export,ANY,BigBedFile,ANY-method export,GenomicRanges,BigBedFile,ANY-method export.bb export.bb,ANY-method import,BigBedFile,ANY,ANY-method import.bb import.bb,ANY-method seqinfo,BigBedFile-method
Selection of ranges and columnsBigBedSelection BigBedSelection-class coerce,GenomicRanges,BigBedSelection-method coerce,IntegerRangesList,BigBedSelection-method
BigWig Import and ExportBigWigFile BigWigFile-class BigWigFileList BigWigFileList-class BWFile BWFile-class class:BigWigFile class:BigWigFileList class:BWFile cleanupBigWigCache export,ANY,BigWigFile,ANY-method export,GenomicRanges,BigWigFile,ANY-method export,List,BigWigFile,ANY-method export.bw export.bw,ANY-method import,BigWigFile,ANY,ANY-method import.bw import.bw,ANY-method path,BigWigFileList-method seqinfo,BigWigFile-method summary,BigWigFile-method
Selection of ranges and columnsBigWigSelection BigWigSelection-class coerce,GenomicRanges,BigWigSelection-method coerce,IntegerRangesList,BigWigSelection-method
Get blocks/exonsblocks blocks,GenomicRanges-method blocks-methods
Browse a genomebrowseGenome browseGenome,GenomicRanges_OR_GenomicRangesList-method browseGenome,missing-method
Class "BrowserSession"BrowserSession-class genome,BrowserSession-method genome<-,BrowserSession-method names,BrowserSession-method range,BrowserSession-method show,BrowserSession-method trackNames,BrowserSession-method
Get a genome browser sessionbrowserSession browserSession,BrowserView-method browserSession,character-method browserSession,missing-method browserSession-methods
Class "BrowserView"BrowserView-class show,BrowserView-method visible visible,BrowserView-method visible<- visible<-,BrowserView-method
Getting browser viewsbrowserView browserView,UCSCSession-method browserView-methods
Lists of BrowserViewBrowserViewList BrowserViewList-class
Getting the browser viewsbrowserViews browserViews,UCSCSession-method browserViews-methods
Chain objectsChain-class ChainBlock-class ChainFile ChainFile-class class:Chain class:ChainBlock class:ChainFile import,ChainFile,ANY,ANY-method import.chain import.chain,ANY-method offset,ChainBlock-method ranges,ChainBlock-method reversed reversed,ChainBlock-method score,ChainBlock-method space,ChainBlock-method
CPNE1 SNP trackcpneTrack
FastaFile objectsclass:FastaFile export,ANY,FastaFile,ANY-method export,XStringSet,FastaFile,ANY-method FastaFile FastaFile-class import,FastaFile,ANY,ANY-method
Get available genome browsersgenomeBrowsers
Data on a Genomechrom chrom,GRanges-method chrom<- chrom<-,GRanges-method GenomicData score,ANY-method
Genomic data selectionGenomicSelection
GFFFile objectsclass:GFF1File class:GFF2File class:GFF3File class:GFFFile class:GTFFile class:GVFFile export,ANY,GFFFile,ANY-method export,GenomicRanges,GFFFile,ANY-method export,GenomicRangesList,GFFFile,ANY-method export,GRangesList,GFFFile,ANY-method export,GRangesList,GTFFile,ANY-method export.gff export.gff,ANY-method export.gff1 export.gff1,ANY-method export.gff2 export.gff2,ANY-method export.gff3 export.gff3,ANY-method genome,GFFFile-method GFF1File GFF1File-class GFF2File GFF2File-class GFF3File GFF3File-class GFFFile GFFFile-class GTFFile GTFFile-class GVFFile GVFFile-class import,GFFFile,ANY,ANY-method import.gff import.gff,ANY-method import.gff1 import.gff1,ANY-method import.gff2 import.gff2,ANY-method import.gff3 import.gff3,ANY-method
GRanges for a GenomeGRangesForBSGenome GRangesForUCSCGenome SeqinfoForBSGenome SeqinfoForUCSCGenome
Class "GraphTrackLine"coerce,BasicTrackLine,GraphTrackLine-method coerce,character,GraphTrackLine-method coerce,GraphTrackLine,BasicTrackLine-method coerce,GraphTrackLine,character-method GraphTrackLine-class
Ranges on a Genomechrom,IntegerRangesList-method chrom<-,IntegerRangesList-method IntegerRangesList-methods
Lift intervals between genome buildsliftOver liftOver,ANY,ANY-method liftOver,GenomicRanges,Chain-method liftOver,Pairs,Chain-method
Quickload Access$,Quickload-method class:Quickload coerce,character,Quickload-method genome,Quickload-method length,Quickload-method Quickload Quickload-class show,Quickload-method [[,Quickload,ANY,ANY-method
Quickload Genome Accessclass:QuickloadGenome genome,QuickloadGenome-method length,QuickloadGenome-method mcols,QuickloadGenome-method names,QuickloadGenome-method organism,QuickloadGenome-method quickload QuickloadGenome QuickloadGenome-class referenceSequence referenceSequence,QuickloadGenome-method referenceSequence<- referenceSequence<-,QuickloadGenome-method releaseDate,QuickloadGenome-method seqinfo,DNAStringSet-method seqinfo,QuickloadGenome-method seqinfo<-,QuickloadGenome-method show,QuickloadGenome-method track,QuickloadGenome-method track<-,QuickloadGenome,ANY-method track<-,QuickloadGenome,BiocFile-method track<-,QuickloadGenome,character-method track<-,QuickloadGenome,RsamtoolsFile-method uri,QuickloadGenome-method
Reads a file in GFF formatGFFcolnames readGFF
Load a sequencesequence<- sequence<--methods
TabixFile Import/Exportexport,ANY,TabSeparatedFile,ANY-method export,GenomicRanges,TabSeparatedFile,ANY-method exportToTabix exportToTabix,ANY,character-method import,TabixFile,ANY,ANY-method
microRNA target sitestargets
Laying trackstrack<- track<-,BrowserSession,ANY-method track<--methods
Track Databases$,TrackDb-method $<-,TrackDb-method class:TrackDb track<-,TrackDb,ANY-method TrackDb-class [[,TrackDb,ANY,ANY-method [[<-,TrackDb,ANY,ANY-method
TrackHub Access$,TrackHub-method class:TrackHub coerce,character,TrackHub-method descriptionUrl,TrackHub-method descriptionUrl<-,TrackHub-method email,TrackHub-method email<-,TrackHub-method genome,TrackHub-method genomeField,TrackHub-method genomeField<-,TrackHub-method genomeFile,TrackHub-method genomeFile<-,TrackHub-method genomeInfo,TrackHub-method genomeInfo<-,TrackHub-method hub,TrackHub-method hub<-,TrackHub-method length,TrackHub-method longLabel,TrackHub-method longLabel<-,TrackHub-method shortLabel,TrackHub-method shortLabel<-,TrackHub-method show,TrackHub-method TrackHub TrackHub-class uri writeTrackHub [[,TrackHub,ANY,ANY-method
TrackHub Genome Accessclass:TrackHubGenome genome,TrackHubGenome-method getTracks,TrackHubGenome-method length,TrackHubGenome-method names,TrackHubGenome-method organism,TrackHubGenome-method referenceSequence,TrackHubGenome-method referenceSequence<-,TrackHubGenome-method show,TrackHubGenome-method track,TrackHubGenome-method track<-,TrackHubGenome,ANY-method track<-,TrackHubGenome,character-method track<-,TrackHubGenome,RsamtoolsFile-method track<-,TrackHubGenome,RTLFile-method trackField,TrackHubGenome-method trackField<-,TrackHubGenome-method trackhub TrackHubGenome TrackHubGenome-class uri,TrackHubGenome-method writeTrackHub,TrackHubGenome-method
Class "TrackLine"coerce,character,TrackLine-method coerce,TrackLine,character-method show,TrackLine-method TrackLine-class
Accessing track namestrackNames trackNames,UCSCSession-method trackNames,UCSCTrackModes-method trackNames,UCSCView-method trackNames-methods trackNames<- trackNames<-,UCSCTrackModes-method trackNames<-,UCSCView-method trackNames<--methods
2bit Files2BitFile 2BitFile-class class:2BitFile class:TwoBitFile export,ANY,TwoBitFile,ANY-method export,DNAStringSet,character,ANY-method export,DNAStringSet,TwoBitFile,ANY-method export.2bit export.2bit,ANY-method getSeq,TwoBitFile-method import,TwoBitFile,ANY,ANY-method import.2bit import.2bit,ANY-method seqinfo,TwoBitFile-method TwoBitFile TwoBitFile-class
Class "UCSCData"coerce,GRanges,UCSCData-method coerce,UCSCData,GRanges-method export.bed,UCSCData,character_OR_connection-method export.bed15,UCSCData-method export.gff,UCSCData,character_OR_connection-method export.ucsc,UCSCData,character_OR_connection-method initialize,UCSCData-method show,UCSCData-method split,UCSCData,ANY-method split,UCSCData,Vector-method UCSCData-class
UCSCFile objectsclass:UCSCFile export,ANY,UCSCFile,ANY-method export,GenomicRanges,UCSCFile,ANY-method export,GenomicRangesList,UCSCFile,ANY-method export,UCSCData,UCSCFile,ANY-method export.ucsc export.ucsc,ANY,ANY-method export.ucsc,ANY,BiocFile-method import,UCSCFile,ANY,ANY-method import.ucsc import.ucsc,ANY-method import.ucsc,BiocFile-method UCSCFile UCSCFile-class
Get available genomes on UCSCucscGenomes
UCSC Schemagenome,UCSCSchema-method nrow,UCSCSchema-method tableName,UCSCSchema-method ucscSchema,UCSCSchemaDescription-method UCSCSchema-class
Class "UCSCSession"genome,ucscCart-method genome,UCSCSession-method genome<-,UCSCSession-method getTable,UCSCSession-method initialize,UCSCSession-method range,ucscCart-method range,UCSCSession-method range<- range<-,UCSCSession-method seqinfo,UCSCSession-method track,UCSCSession-method track<-,UCSCSession,BiocFile-method track<-,UCSCSession,GenomicRangesList-method UCSCSession-class
Querying UCSC Tablesgenome,UCSCTableQuery-method genome<-,UCSCTableQuery-method getTable getTable,UCSCTableQuery-method hubUrl hubUrl,UCSCTableQuery-method hubUrl<-,UCSCTableQuery-method names,UCSCTableQuery-method names<-,UCSCTableQuery-method range,UCSCTableQuery-method range<-,UCSCTableQuery-method show,UCSCTableQuery-method tableName tableName,UCSCTableQuery-method tableName<- tableName<-,UCSCTableQuery-method tableNames tableNames,UCSCTableQuery-method track track,UCSCTableQuery-method ucscSchema ucscSchema,UCSCTableQuery-method ucscTableQuery ucscTableQuery,character-method ucscTableQuery,UCSCSession-method UCSCTableQuery-class ucscTables
Class "UCSCTrackModes"UCSCTrackModes-class [,UCSCTrackModes,ANY,ANY,ANY-method [<-,UCSCTrackModes,ANY,ANY,ANY-method
Accessing UCSC track modesucscTrackModes ucscTrackModes,character-method ucscTrackModes,missing-method ucscTrackModes,UCSCSession-method ucscTrackModes,ucscTracks-method ucscTrackModes,UCSCView-method ucscTrackModes-methods ucscTrackModes<- ucscTrackModes<-,UCSCView,character-method ucscTrackModes<-,UCSCView,UCSCTrackModes-method ucscTrackModes<--methods
Class "UCSCView"range,UCSCView-method range<-,UCSCView-method UCSCView-class viewURL visible,UCSCView-method visible<-,UCSCView-method
WIG Import and Exportclass:WIGFile export,ANY,WIGFile,ANY-method export,GenomicRanges,WIGFile,ANY-method export,GenomicRangesList,WIGFile,ANY-method export,UCSCData,WIGFile,ANY-method export.wig export.wig,ANY-method import,WIGFile,ANY,ANY-method import.wig import.wig,ANY-method WIGFile WIGFile-class
Convert WIG to BigWigwigToBigWig