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.
|Author||Michael Lawrence, Vince Carey, Robert Gentleman|
|Date of publication||None|
|Maintainer||Michael Lawrence <firstname.lastname@example.org>|
|License||Artistic-2.0 + file LICENSE|
activeView-methods: Accessing the active view
asBED: Coerce to BED structure
asGFF: Coerce to GFF structure
BamFile-methods: Export to BAM Files
basicTrackLine-class: Class "BasicTrackLine"
Bed15TrackLine-class: Class "Bed15TrackLine"
BEDFile-class: BEDFile objects
BigWigFile: BigWig Import and Export
BigWigSelection-class: Selection of ranges and columns
blocks-methods: Get blocks/exons
browseGenome: Browse a genome
browserSession-class: Class "BrowserSession"
browserSession-methods: Get a genome browser session
browserView-class: Class "BrowserView"
BrowserViewList-class: Lists of BrowserView
browserView-methods: Getting browser views
browserViews-methods: Getting the browser views
Chain-class: Chain objects
cpneTrack: CPNE1 SNP track
export: Import and export
FastaFile-class: FastaFile objects
genomeBrowsers: Get available genome browsers
GenomicData: Data on a Genome
GenomicSelection: Genomic data selection
GFFFile-class: GFFFile objects
GRangesForUCSCGenome: GRanges for a Genome
laySequence-methods: Load a sequence
layTrack-methods: Laying tracks
liftOver: Lift intervals between genome builds
Quickload-class: Quickload Access
QuickloadGenome-class: Quickload Genome Access
RangesList-methods: Ranges on a Genome
readGFF: Reads a file in GFF format
RTLFile-class: RTLFile objects
TabixFile-methods: TabixFile Import/Export
targets: microRNA target sites
TrackDb-class: Track Databases
tracks-methods: Accessing track names
TwoBitFile-class: 2bit Files
UCSCData-class: Class "UCSCData"
UCSCFile-class: UCSCFile objects
ucscGenomes: Get available genomes on UCSC
UCSCSchema-class: UCSC Schema
ucscSession-class: Class "UCSCSession"
UCSCTableQuery-class: Querying UCSC Tables
ucscTrackLine-class: Class "TrackLine"
ucscTrackModes-class: Class "UCSCTrackModes"
ucscTrackModes-methods: Accessing UCSC track modes
ucscView-class: Class "UCSCView"
WIGFile-class: WIG Import and Export
wigToBigWig: Convert WIG to BigWig
wigTrackLine-class: Class "GraphTrackLine"