Package: rtracklayer 1.73.0

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

rtracklayer_1.73.0.tar.gz
rtracklayer_1.73.0.zip(r-4.7)rtracklayer_1.73.0.zip(r-4.6)rtracklayer_1.73.0.zip(r-4.5)
rtracklayer_1.73.0.tgz(r-4.6-x86_64)rtracklayer_1.73.0.tgz(r-4.6-arm64)rtracklayer_1.73.0.tgz(r-4.5-x86_64)rtracklayer_1.73.0.tgz(r-4.5-arm64)
rtracklayer_1.73.0.tar.gz(r-4.7-arm64)rtracklayer_1.73.0.tar.gz(r-4.7-x86_64)rtracklayer_1.73.0.tar.gz(r-4.6-arm64)rtracklayer_1.73.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
rtracklayer/json (API)

# Install 'rtracklayer' in R:

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

Uses libs:

zlib– Compression library
openssl– Secure Sockets Layer toolkit
curl– Easy-to-use client-side URL transfer library

Datasets:

cpneTrack - CPNE1 SNP track
targets - MicroRNA target sites

On BioConductor:rtracklayer-1.73.0(bioc 3.24)rtracklayer-1.72.0(bioc 3.23)

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

annotation visualization dataimport zlib openssl curl

11.37 score 511 packages 14k scripts 107 mentions 161 exports 48 dependencies

Last updated from:c524fdf64d. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	627
linux-devel-arm64	WARNING	675
linux-devel-x86_64	WARNING	786
source / vignettes	OK	784
linux-release-arm64	WARNING	634
linux-release-x86_64	WARNING	757
macos-release-arm64	WARNING	288
macos-release-x86_64	WARNING	527
macos-oldrel-arm64	WARNING	428
macos-oldrel-x86_64	WARNING	685
windows-devel	WARNING	528
windows-release	WARNING	519
windows-oldrel	WARNING	537
wasm-release	FAIL	396

Exports:activeView activeView<-as.data.frame asBED asGFF BED15File BEDFile BEDGraphFile BEDPEFile BigBedFile BigBedSelection BigWigFile BigWigFileList BigWigSelection blocks browseGenome browserSession browserSession<-browserView browserViews ChainFile chrom chrom<-cleanupBigBedCache cleanupBigWigCache close coerce descriptionUrl descriptionUrl<-email email<-end end<-export export.2bit export.bb export.bed export.bed15 export.bedGraph export.bw export.gff export.gff1 export.gff2 export.gff3 export.ucsc export.wig exportToTabix FastaFile fileFormat genome Genome genome<-genomeBrowsers genomeField genomeField<-genomeInfo genomeInfo<-genomesFile genomesFile<-GenomicData GenomicSelection getSeq getTable getTracks GFF1File GFF2File GFF3File GFFcolnames GFFFile GRangesForBSGenome GRangesForUCSCGenome GTFFile GVFFile hub hub<-hubUrl hubUrl<-import import.2bit import.bb import.bed import.bed15 import.bedGraph import.bw import.chain import.gff import.gff1 import.gff2 import.gff3 import.ucsc import.wig initialize liftOver longLabel longLabel<-mcols nrow offset organism path quickload Quickload QuickloadGenome range<-ranges readGFF readGFFAsGRanges readGFFPragmas referenceSequence referenceSequence<-releaseDate resource reversed score score<-seqinfo seqinfo<-SeqinfoForBSGenome SeqinfoForUCSCGenome shortLabel shortLabel<-show sniffGFFVersion space split start start<-strand summary tableName tableName<-tableNames track Track track<-TrackContainer trackField trackField<-trackhub TrackHub TrackHubGenome trackNames trackNames<-TwoBitFile UCSCFile ucscGenomes ucscSchema ucscTableQuery ucscTables ucscTrackModes ucscTrackModes<-uri values viewURL visible visible<-width width<-WIGFile wigToBigWig writeTrackHub

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys XML XVector yaml

rtracklayer

Rendered fromrtracklayer.Rnwusingutils::Sweave

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Accessing the active view	activeView activeView,BrowserSession-method activeView,UCSCView-method activeView-methods activeView<- activeView<--methods
Coerce to BED structure	asBED asBED,GAlignments-method asBED,GRangesList-method
Coerce to GFF structure	asGFF asGFF,GRangesList-method
Export to BAM Files	export,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 fileFormat,TrackLine-method
Class "Bed15TrackLine"	Bed15TrackLine-class coerce,Bed15TrackLine,character-method coerce,character,Bed15TrackLine-method fileFormat,Bed15TrackLine-method
BEDFile objects	BED15File 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,CompressedGRangesList,BEDFile,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,SimpleGRangesList,BEDFile,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 Export	BBFile 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 columns	BigBedSelection BigBedSelection-class coerce,GenomicRanges,BigBedSelection-method coerce,IntegerRangesList,BigBedSelection-method
BigWig Import and Export	BigWigFile 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 columns	BigWigSelection BigWigSelection-class coerce,GenomicRanges,BigWigSelection-method coerce,IntegerRangesList,BigWigSelection-method
Get blocks/exons	blocks blocks,GenomicRanges-method blocks-methods
Browse a genome	browseGenome 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 session	browserSession 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 views	browserView browserView,UCSCSession-method browserView-methods
Lists of BrowserView	BrowserViewList BrowserViewList-class
Getting the browser views	browserViews browserViews,UCSCSession-method browserViews-methods
Chain objects	Chain-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 track	cpneTrack
FastaFile objects	class:FastaFile export,ANY,FastaFile,ANY-method export,XStringSet,FastaFile,ANY-method FastaFile FastaFile-class import,FastaFile,ANY,ANY-method
Get available genome browsers	genomeBrowsers
Data on a Genome	chrom chrom,GRanges-method chrom<- chrom<-,GRanges-method GenomicData score,ANY-method
Genomic data selection	GenomicSelection
GFFFile objects	class:GFF1File class:GFF2File class:GFF3File class:GFFFile class:GTFFile class:GVFFile export,ANY,GFFFile,ANY-method export,CompressedGRangesList,GFFFile,ANY-method export,GenomicRanges,GFFFile,ANY-method export,GenomicRangesList,GFFFile,ANY-method export,GRangesList,GTFFile,ANY-method export,SimpleGRangesList,GFFFile,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 Genome	GRangesForBSGenome GRangesForUCSCGenome SeqinfoForBSGenome SeqinfoForUCSCGenome
Class "GraphTrackLine"	coerce,BasicTrackLine,GraphTrackLine-method coerce,character,GraphTrackLine-method coerce,GraphTrackLine,BasicTrackLine-method coerce,GraphTrackLine,character-method fileFormat,GraphTrackLine-method GraphTrackLine-class
Ranges on a Genome	chrom,IntegerRangesList-method chrom<-,IntegerRangesList-method IntegerRangesList-methods
Lift intervals between genome builds	liftOver liftOver,ANY,ANY-method liftOver,GenomicRanges,Chain-method liftOver,GRangesList,Chain-method liftOver,Pairs,Chain-method
Quickload Access	$,Quickload-method class:Quickload coerce,character,Quickload-method genome,Quickload-method length,Quickload-method names,Quickload-method Quickload Quickload-class show,Quickload-method uri,Quickload-method [[,Quickload,ANY,ANY-method
Quickload Genome Access	class: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 trackNames,QuickloadGenome-method uri,QuickloadGenome-method
Reads a file in GFF format	GFFcolnames readGFF
Load a sequence	sequence<- sequence<--methods
TabixFile Import/Export	export,ANY,TabSeparatedFile,ANY-method export,GenomicRanges,TabSeparatedFile,ANY-method exportToTabix exportToTabix,ANY,character-method import,TabixFile,ANY,ANY-method
microRNA target sites	targets
Laying tracks	track<- 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 Access	class: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 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 names	trackNames trackNames,UCSCSession-method trackNames,UCSCTrackModes-method trackNames,UCSCView-method trackNames-methods trackNames<- trackNames<-,UCSCTrackModes-method trackNames<-,UCSCView-method trackNames<--methods
2bit Files	2BitFile 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 objects	class:UCSCFile export,ANY,UCSCFile,ANY-method export,GenomicRanges,UCSCFile,ANY-method export,GenomicRangesList,UCSCFile,ANY-method export,GRangesList,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 UCSC	ucscGenomes
UCSC Schema	genome,UCSCSchema-method nrow,UCSCSchema-method show,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,SimpleGRangesList-method UCSCSession-class
Querying UCSC Tables	browserSession,UCSCTableQuery-method browserSession<- browserSession<-,UCSCTableQuery-method genome,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 modes	ucscTrackModes 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 Export	class:WIGFile export,ANY,WIGFile,ANY-method export,GenomicRanges,WIGFile,ANY-method export,SimpleGRangesList,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 BigWig	wigToBigWig