R interface to genome annotation files and the UCSC genome
browser
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Documentation for package ‘rtracklayer’ version 1.54.0
- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
A B C D E F G H I L M N O P Q R S T U V W misc
-- A --
| activeView | Accessing the active view |
| activeView-method | Accessing the active view |
| activeView-methods | Accessing the active view |
| activeView<- | Accessing the active view |
| activeView<--methods | Accessing the active view |
| asBED | Coerce to BED structure |
| asBED-method | Coerce to BED structure |
| asGFF | Coerce to GFF structure |
| asGFF-method | Coerce to GFF structure |
-- B --
| BasicTrackLine-class | Class "BasicTrackLine" |
| BBFile | BigBed Import and Export |
| BBFile-class | BigBed Import and Export |
| BED15File | BEDFile objects |
| BED15File-class | BEDFile objects |
| Bed15TrackLine-class | Class "Bed15TrackLine" |
| BEDFile | BEDFile objects |
| BEDFile-class | BEDFile objects |
| BEDGraphFile | BEDFile objects |
| BEDGraphFile-class | BEDFile objects |
| BEDPEFile | BEDFile objects |
| BEDPEFile-class | BEDFile objects |
| BigBedFile | BigBed Import and Export |
| BigBedFile-class | BigBed Import and Export |
| BigBedSelection | Selection of ranges and columns |
| BigBedSelection-class | Selection of ranges and columns |
| BigWigFile | BigWig Import and Export |
| BigWigFile-class | BigWig Import and Export |
| BigWigFileList | BigWig Import and Export |
| BigWigFileList-class | BigWig Import and Export |
| BigWigSelection | Selection of ranges and columns |
| BigWigSelection-class | Selection of ranges and columns |
| blocks | Get blocks/exons |
| blocks-method | Get blocks/exons |
| blocks-methods | Get blocks/exons |
| BroadPeakFile | BEDFile objects |
| BroadPeakFile-class | BEDFile objects |
| browseGenome | Browse a genome |
| browseGenome-method | Browse a genome |
| browserSession | Get a genome browser session |
| BrowserSession-class | Class "BrowserSession" |
| browserSession-method | Get a genome browser session |
| browserSession-methods | Get a genome browser session |
| browserView | Getting browser views |
| BrowserView-class | Class "BrowserView" |
| browserView-method | Getting browser views |
| browserView-methods | Getting browser views |
| BrowserViewList | Lists of BrowserView |
| BrowserViewList-class | Lists of BrowserView |
| browserViews | Getting the browser views |
| browserViews-method | Getting the browser views |
| browserViews-methods | Getting the browser views |
| BWFile | BigWig Import and Export |
| BWFile-class | BigWig Import and Export |
-- C --
| Chain-class | Chain objects |
| ChainBlock-class | Chain objects |
| ChainFile | Chain objects |
| ChainFile-class | Chain objects |
| chrom | Data on a Genome |
| chrom-method | Data on a Genome |
| chrom-method | Ranges on a Genome |
| chrom<- | Data on a Genome |
| chrom<--method | Data on a Genome |
| chrom<--method | Ranges on a Genome |
| class:2BitFile | 2bit Files |
| class:BBFile | BigBed Import and Export |
| class:BED15File | BEDFile objects |
| class:BEDFile | BEDFile objects |
| class:BEDGraphFile | BEDFile objects |
| class:BigBedFile | BigBed Import and Export |
| class:BigWigFile | BigWig Import and Export |
| class:BigWigFileList | BigWig Import and Export |
| class:BroadPeakFile | BEDFile objects |
| class:BWFile | BigWig Import and Export |
| class:Chain | Chain objects |
| class:ChainBlock | Chain objects |
| class:ChainFile | Chain objects |
| class:FastaFile | FastaFile objects |
| class:GFF1File | GFFFile objects |
| class:GFF2File | GFFFile objects |
| class:GFF3File | GFFFile objects |
| class:GFFFile | GFFFile objects |
| class:GTFFile | GFFFile objects |
| class:GVFFile | GFFFile objects |
| class:NarrowPeakFile | BEDFile objects |
| class:Quickload | Quickload Access |
| class:QuickloadGenome | Quickload Genome Access |
| class:TrackDb | Track Databases |
| class:TrackHub | TrackHub Access |
| class:TrackHubGenome | TrackHub Genome Access |
| class:TwoBitFile | 2bit Files |
| class:UCSCFile | UCSCFile objects |
| class:WIGFile | WIG Import and Export |
| cleanupBigWigCache | BigWig Import and Export |
| coerce-method | Class "Bed15TrackLine" |
| coerce-method | Selection of ranges and columns |
| coerce-method | Selection of ranges and columns |
| coerce-method | Quickload Access |
| coerce-method | TrackHub Access |
| coerce-method | Class "UCSCData" |
| coerce-method | Class "BasicTrackLine" |
| coerce-method | Class "TrackLine" |
| coerce-method | Class "GraphTrackLine" |
| cpneTrack | CPNE1 SNP track |
-- D --
| descriptionUrl-method | TrackHub Access |
| descriptionUrl<--method | TrackHub Access |
-- E --
| email-method | TrackHub Access |
| email<--method | TrackHub Access |
| export-method | BEDFile objects |
| export-method | Export to BAM Files |
| export-method | BigBed Import and Export |
| export-method | BigWig Import and Export |
| export-method | FastaFile objects |
| export-method | GFFFile objects |
| export-method | TabixFile Import/Export |
| export-method | 2bit Files |
| export-method | UCSCFile objects |
| export-method | WIG Import and Export |
| export.2bit | 2bit Files |
| export.2bit-method | 2bit Files |
| export.bb | BigBed Import and Export |
| export.bb-method | BigBed Import and Export |
| export.bed | BEDFile objects |
| export.bed-method | BEDFile objects |
| export.bed-method | Class "UCSCData" |
| export.bed15 | BEDFile objects |
| export.bed15-method | BEDFile objects |
| export.bed15-method | Class "UCSCData" |
| export.bedGraph | BEDFile objects |
| export.bedGraph-method | BEDFile objects |
| export.bw | BigWig Import and Export |
| export.bw-method | BigWig Import and Export |
| export.gff | GFFFile objects |
| export.gff-method | GFFFile objects |
| export.gff-method | Class "UCSCData" |
| export.gff1 | GFFFile objects |
| export.gff1-method | GFFFile objects |
| export.gff2 | GFFFile objects |
| export.gff2-method | GFFFile objects |
| export.gff3 | GFFFile objects |
| export.gff3-method | GFFFile objects |
| export.ucsc | UCSCFile objects |
| export.ucsc-method | Class "UCSCData" |
| export.ucsc-method | UCSCFile objects |
| export.wig | WIG Import and Export |
| export.wig-method | WIG Import and Export |
| exportToTabix | TabixFile Import/Export |
| exportToTabix-method | TabixFile Import/Export |
-- F --
| FastaFile | FastaFile objects |
| FastaFile-class | FastaFile objects |
-- G --
| genome-method | GFFFile objects |
| genome-method | Quickload Access |
| genome-method | Quickload Genome Access |
| genome-method | TrackHub Access |
| genome-method | TrackHub Genome Access |
| genome-method | UCSC Schema |
| genome-method | Querying UCSC Tables |
| genome-method | Class "BrowserSession" |
| genome-method | Class "UCSCSession" |
| genome<--method | Querying UCSC Tables |
| genome<--method | Class "BrowserSession" |
| genome<--method | Class "UCSCSession" |
| genomeBrowsers | Get available genome browsers |
| genomeField-method | TrackHub Access |
| genomeField<--method | TrackHub Access |
| genomeFile-method | TrackHub Access |
| genomeFile<--method | TrackHub Access |
| genomeInfo-method | TrackHub Access |
| genomeInfo<--method | TrackHub Access |
| GenomicData | Data on a Genome |
| GenomicSelection | Genomic data selection |
| getSeq-method | 2bit Files |
| getTable | Querying UCSC Tables |
| getTable-method | Querying UCSC Tables |
| getTable-method | Class "UCSCSession" |
| getTracks-method | TrackHub Genome Access |
| GFF1File | GFFFile objects |
| GFF1File-class | GFFFile objects |
| GFF2File | GFFFile objects |
| GFF2File-class | GFFFile objects |
| GFF3File | GFFFile objects |
| GFF3File-class | GFFFile objects |
| GFFcolnames | Reads a file in GFF format |
| GFFFile | GFFFile objects |
| GFFFile-class | GFFFile objects |
| GRangesForBSGenome | GRanges for a Genome |
| GRangesForUCSCGenome | GRanges for a Genome |
| GraphTrackLine-class | Class "GraphTrackLine" |
| GTFFile | GFFFile objects |
| GTFFile-class | GFFFile objects |
| GVFFile | GFFFile objects |
| GVFFile-class | GFFFile objects |
-- H --
| hub-method | TrackHub Access |
| hub<--method | TrackHub Access |
| hubUrl | Querying UCSC Tables |
| hubUrl-method | Querying UCSC Tables |
| hubUrl<--method | Querying UCSC Tables |
-- I --
| import-method | BEDFile objects |
| import-method | Export to BAM Files |
| import-method | BigBed Import and Export |
| import-method | BigWig Import and Export |
| import-method | Chain objects |
| import-method | FastaFile objects |
| import-method | GFFFile objects |
| import-method | TabixFile Import/Export |
| import-method | 2bit Files |
| import-method | UCSCFile objects |
| import-method | WIG Import and Export |
| import.2bit | 2bit Files |
| import.2bit-method | 2bit Files |
| import.bb | BigBed Import and Export |
| import.bb-method | BigBed Import and Export |
| import.bed | BEDFile objects |
| import.bed-method | BEDFile objects |
| import.bed15 | BEDFile objects |
| import.bed15-method | BEDFile objects |
| import.bedGraph | BEDFile objects |
| import.bedGraph-method | BEDFile objects |
| import.BroadPeak | BEDFile objects |
| import.BroadPeak-method | BEDFile objects |
| import.bw | BigWig Import and Export |
| import.bw-method | BigWig Import and Export |
| import.chain | Chain objects |
| import.chain-method | Chain objects |
| import.gff | GFFFile objects |
| import.gff-method | GFFFile objects |
| import.gff1 | GFFFile objects |
| import.gff1-method | GFFFile objects |
| import.gff2 | GFFFile objects |
| import.gff2-method | GFFFile objects |
| import.gff3 | GFFFile objects |
| import.gff3-method | GFFFile objects |
| import.NarrowPeak | BEDFile objects |
| import.NarrowPeak-method | BEDFile objects |
| import.ucsc | UCSCFile objects |
| import.ucsc-method | UCSCFile objects |
| import.wig | WIG Import and Export |
| import.wig-method | WIG Import and Export |
| initialize-method | Class "UCSCData" |
| initialize-method | Class "UCSCSession" |
| IntegerRangesList-methods | Ranges on a Genome |
-- L --
| length-method | Quickload Access |
| length-method | Quickload Genome Access |
| length-method | TrackHub Access |
| length-method | TrackHub Genome Access |
| liftOver | Lift intervals between genome builds |
| liftOver-method | Lift intervals between genome builds |
| longLabel-method | TrackHub Access |
| longLabel<--method | TrackHub Access |
-- M --
| mcols-method | Quickload Genome Access |
-- N --
| names-method | Quickload Genome Access |
| names-method | TrackHub Genome Access |
| names-method | Querying UCSC Tables |
| names-method | Class "BrowserSession" |
| names<--method | Querying UCSC Tables |
| NarrowPeakFile | BEDFile objects |
| NarrowPeakFile-class | BEDFile objects |
| nrow-method | UCSC Schema |
-- O --
| offset-method | Chain objects |
| organism-method | Quickload Genome Access |
| organism-method | TrackHub Genome Access |
-- P --
| path-method | BigWig Import and Export |
-- Q --
| Quickload | Quickload Access |
| quickload | Quickload Genome Access |
| Quickload-class | Quickload Access |
| QuickloadGenome | Quickload Genome Access |
| QuickloadGenome-class | Quickload Genome Access |
-- R --
| range-method | Querying UCSC Tables |
| range-method | Class "BrowserSession" |
| range-method | Class "UCSCSession" |
| range-method | Class "UCSCView" |
| range<- | Class "UCSCSession" |
| range<--method | Querying UCSC Tables |
| range<--method | Class "UCSCSession" |
| range<--method | Class "UCSCView" |
| ranges-method | Chain objects |
| readGFF | Reads a file in GFF format |
| referenceSequence | Quickload Genome Access |
| referenceSequence-method | Quickload Genome Access |
| referenceSequence-method | TrackHub Genome Access |
| referenceSequence<- | Quickload Genome Access |
| referenceSequence<--method | Quickload Genome Access |
| referenceSequence<--method | TrackHub Genome Access |
| releaseDate-method | Quickload Genome Access |
| reversed | Chain objects |
| reversed-method | Chain objects |
-- S --
| score-method | Chain objects |
| score-method | Data on a Genome |
| seqinfo-method | BigBed Import and Export |
| seqinfo-method | BigWig Import and Export |
| seqinfo-method | Quickload Genome Access |
| seqinfo-method | 2bit Files |
| seqinfo-method | Class "UCSCSession" |
| seqinfo<--method | Quickload Genome Access |
| SeqinfoForBSGenome | GRanges for a Genome |
| SeqinfoForUCSCGenome | GRanges for a Genome |
| sequence<- | Load a sequence |
| sequence<--methods | Load a sequence |
| shortLabel-method | TrackHub Access |
| shortLabel<--method | TrackHub Access |
| show-method | Quickload Access |
| show-method | Quickload Genome Access |
| show-method | TrackHub Access |
| show-method | TrackHub Genome Access |
| show-method | Class "UCSCData" |
| show-method | Querying UCSC Tables |
| show-method | Class "BrowserSession" |
| show-method | Class "BrowserView" |
| show-method | Class "TrackLine" |
| space-method | Chain objects |
| split-method | Class "UCSCData" |
| summary-method | BigWig Import and Export |
-- T --
| tableName | Querying UCSC Tables |
| tableName-method | UCSC Schema |
| tableName-method | Querying UCSC Tables |
| tableName<- | Querying UCSC Tables |
| tableName<--method | Querying UCSC Tables |
| tableNames | Querying UCSC Tables |
| tableNames-method | Querying UCSC Tables |
| targets | microRNA target sites |
| track | Querying UCSC Tables |
| track-method | Quickload Genome Access |
| track-method | TrackHub Genome Access |
| track-method | Querying UCSC Tables |
| track-method | Class "UCSCSession" |
| track<- | Laying tracks |
| track<--method | Quickload Genome Access |
| track<--method | Track Databases |
| track<--method | TrackHub Genome Access |
| track<--method | Laying tracks |
| track<--method | Class "UCSCSession" |
| track<--methods | Laying tracks |
| TrackDb-class | Track Databases |
| trackField-method | TrackHub Genome Access |
| trackField<--method | TrackHub Genome Access |
| TrackHub | TrackHub Access |
| trackhub | TrackHub Genome Access |
| TrackHub-class | TrackHub Access |
| TrackHubGenome | TrackHub Genome Access |
| TrackHubGenome-class | TrackHub Genome Access |
| TrackLine-class | Class "TrackLine" |
| trackNames | Accessing track names |
| trackNames-method | Class "BrowserSession" |
| trackNames-method | Accessing track names |
| trackNames-methods | Accessing track names |
| trackNames<- | Accessing track names |
| trackNames<--method | Accessing track names |
| trackNames<--methods | Accessing track names |
| TwoBitFile | 2bit Files |
| TwoBitFile-class | 2bit Files |
-- U --
| UCSCData-class | Class "UCSCData" |
| UCSCFile | UCSCFile objects |
| UCSCFile-class | UCSCFile objects |
| ucscGenomes | Get available genomes on UCSC |
| ucscSchema | Querying UCSC Tables |
| UCSCSchema-class | UCSC Schema |
| ucscSchema-method | UCSC Schema |
| ucscSchema-method | Querying UCSC Tables |
| UCSCSession-class | Class "UCSCSession" |
| ucscTableQuery | Querying UCSC Tables |
| UCSCTableQuery-class | Querying UCSC Tables |
| ucscTableQuery-method | Querying UCSC Tables |
| ucscTables | Querying UCSC Tables |
| ucscTrackModes | Accessing UCSC track modes |
| UCSCTrackModes-class | Class "UCSCTrackModes" |
| ucscTrackModes-method | Accessing UCSC track modes |
| ucscTrackModes-methods | Accessing UCSC track modes |
| ucscTrackModes<- | Accessing UCSC track modes |
| ucscTrackModes<--method | Accessing UCSC track modes |
| ucscTrackModes<--methods | Accessing UCSC track modes |
| UCSCView-class | Class "UCSCView" |
| uri | Quickload Access |
| uri | TrackHub Access |
| uri-method | Quickload Genome Access |
| uri-method | TrackHub Genome Access |
-- V --
| viewURL | Class "UCSCView" |
| visible | Class "BrowserView" |
| visible-method | Class "BrowserView" |
| visible-method | Class "UCSCView" |
| visible<- | Class "BrowserView" |
| visible<--method | Class "BrowserView" |
| visible<--method | Class "UCSCView" |
-- W --
| WIGFile | WIG Import and Export |
| WIGFile-class | WIG Import and Export |
| wigToBigWig | Convert WIG to BigWig |
| writeTrackHub | TrackHub Access |
| writeTrackHub-method | TrackHub Genome Access |
-- misc --
| $-method | Quickload Access |
| $-method | Track Databases |
| $-method | TrackHub Access |
| $<--method | Track Databases |
| 2BitFile | 2bit Files |
| 2BitFile-class | 2bit Files |
| [-method | Class "UCSCTrackModes" |
| [<--method | Class "UCSCTrackModes" |
| [[-method | Quickload Access |
| [[-method | Track Databases |
| [[-method | TrackHub Access |
| [[<--method | Track Databases |