rtracklayer v1.32.1

R interface to genome browsers and their annotation tracks

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 in rtracklayer

Name Description
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"
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Details

LinkingTo S4Vectors, IRanges, XVector
License Artistic-2.0 + file LICENSE
Collate io.R web.R ranges.R trackDb.R browser.R ucsc.R readGFF.R gff.R bed.R wig.R utils.R bigWig.R chain.R quickload.R twobit.R fasta.R tabix.R bam.R trackTable.R index.R compression.R test_rtracklayer_package.R ncbi.R
biocViews Annotation,Visualization,DataImport

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