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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.

Functions (56)

BEDFile-class

BEDFile objects

BamFile-methods

Export to BAM Files

Bed15TrackLine-class

Class "Bed15TrackLine"

BigBed Import and Export

BigBedSelection

Selection of ranges and columns

BigWig Import and Export

BigWigSelection-class

Selection of ranges and columns

BrowserViewList-class

Lists of BrowserView

Chain-class

Chain objects

FastaFile-class

FastaFile objects

GFFFile-class

GFFFile objects

GRangesForUCSCGenome

GRanges for a Genome

GenomicData

Data on a Genome

GenomicSelection

Genomic data selection

IntegerRangesList-methods

Ranges on a Genome

Quickload-class

Quickload Access

QuickloadGenome-class

Quickload Genome Access

RTLFile-class

RTLFile objects

TabixFile-methods

TabixFile Import/Export

TrackDb-class

Track Databases

TrackHub-class

TrackHub Access

TrackHubGenome-class

TrackHub Genome Access

TwoBitFile-class

2bit Files

UCSCData-class

Class "UCSCData"

UCSCFile-class

UCSCFile objects

UCSCSchema-class

UCSC Schema

UCSCTableQuery-class

Querying UCSC Tables

WIGFile-class

WIG Import and Export

activeView-methods

Accessing the active view

Coerce to BED structure

Coerce to GFF structure

basicTrackLine-class

Class "BasicTrackLine"

blocks-methods

Get blocks/exons

browseGenome

Browse a genome

browserSession-class

Class "BrowserSession"

browserSession-methods

Get a genome browser session

browserView-class

Class "BrowserView"

browserView-methods

Getting browser views

browserViews-methods

Getting the browser views

CPNE1 SNP track

Import and export

genomeBrowsers

Get available genome browsers

laySequence-methods

Load a sequence

layTrack-methods

Laying tracks

Lift intervals between genome builds

Reads a file in GFF format

microRNA target sites

tracks-methods

Accessing track names

ucscGenomes

Get available genomes on UCSC

ucscSession-class

Class "UCSCSession"

ucscTrackLine-class

Class "TrackLine"

ucscTrackModes-class

Class "UCSCTrackModes"

ucscTrackModes-methods

Accessing UCSC track modes

ucscView-class

Class "UCSCView"

wigToBigWig

Convert WIG to BigWig

wigTrackLine-class

Class "GraphTrackLine"

rtracklayer

R interface to genome annotation files and the UCSC genome browser

v1.50.0

Artistic-2.0 + file LICENSE

Authors

Michael Lawrence, Vince Carey, Robert Gentleman

Initial release

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