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rtracklayer (version 1.32.1)

R interface to genome browsers and their annotation tracks

Description

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.

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Version

Version

1.32.1

License

Artistic-2.0 + file LICENSE

Maintainer

Michael Lawrence

Last Published

February 15th, 2017

Functions in rtracklayer (1.32.1)

BamFile-methods

Export to BAM Files
blocks-methods

Get blocks/exons
asBED

Coerce to BED structure
asGFF

Coerce to GFF structure
BigWigSelection-class

Selection of ranges and columns
BEDFile-class

BEDFile objects
activeView-methods

Accessing the active view
Bed15TrackLine-class

Class "Bed15TrackLine"
BigWigFile-class

BigWig Import and Export
BasicTrackLine-class

Class "BasicTrackLine"
BrowserView-class

Class "BrowserView"
browserView-methods

Getting browser views
browseGenome

Browse a genome
browserViews-methods

Getting the browser views
Chain-class

Chain objects
browserSession-methods

Get a genome browser session
BrowserSession-class

Class "BrowserSession"
BrowserViewList-class

Lists of BrowserView
io

Import and export
cpneTrack

CPNE1 SNP track
GenomicSelection

Genomic data selection
GenomicData

Data on a Genome
liftOver

Lift intervals between genome builds
GFFFile-class

GFFFile objects
Quickload-class

Quickload Access
GRangesForUCSCGenome

GRanges for a Genome
sequence<--methods

Load a sequence
track<--methods

Laying tracks
FastaFile-class

FastaFile objects
genomeBrowsers

Get available genome browsers
RTLFile-class

RTLFile objects
readGFF

Reads a file in GFF format
UCSCTrackModes-class

Class "UCSCTrackModes"
tracks-methods

Accessing track names
ucscTrackModes-methods

Accessing UCSC track modes
UCSCFile-class

UCSCFile objects
TrackDb-class

Track Databases
ucscGenomes

Get available genomes on UCSC
TwoBitFile-class

2bit Files
UCSCData-class

Class "UCSCData"
UCSCTableQuery-class

Querying UCSC Tables
GraphTrackLine-class

Class "GraphTrackLine"
TrackLine-class

Class "TrackLine"
TabixFile-methods

TabixFile Import/Export
wigToBigWig

Convert WIG to BigWig
targets

microRNA target sites
UCSCView-class

Class "UCSCView"
WIGFile-class

WIG Import and Export
QuickloadGenome-class

Quickload Genome Access
RangesList-methods

Ranges on a Genome
UCSCSchema-class

UCSC Schema
UCSCSession-class

Class "UCSCSession"