# A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

## Documentation for package ‘trackViewer’ version 1.44.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

trackViewer-package | Minimal designed plotting tool for genomic data
$-method | Class '"trackStyle"'
$<--method | Class '"trackStyle"'
addArrowMark | Add arrow mark to the figure at a given position
addGuideLine | Add guide lines to the tracks
addInteractionAnnotation | Add annotation markers to the figure at a given position
ARA | Aggregate Region Analysis
browseTracks | browse tracks
browseTracks-shiny | Shiny bindings for browseTracks
browseTracksOutput | Shiny bindings for browseTracks
coverageGR | calculate coverage
dandelion.plot | dandelion.plots
geneModelFromTxdb | Prepare gene model from an object of TxDb
geneTrack | track from TxDb
getCurTrackViewport | Get current track viewport
getGeneIDsFromTxDb | get gene ids by genomic location
getLocation | get genomic location by gene symbol
gi2track | convert GInteractions to track object
gieStain | color sheme for the schema for Chromosome Band (Ideogram)
GIoperator | GInteractions operator
gridPlot | plot GRanges metadata
GRoperator | GRanges operator
ideogramPlot | plot ideogram with data
importBam | Reading data from a BAM file
importData | Reading data from a BED or WIG file to RleList
importGInteractions | Reading data from a ginteractions, hic, cool, or validPairs file
importScore | Reading data from a BED or WIG file
importScSeqScore | plot tracks for single cell RNAseq
listChromosomes | List the available chromosome
listNormalizations | List the available normalizations
listResolutions | List the available resolutions
loadIdeogram | load ideogram from UCSC
lolliplot | Lolliplots
optimizeStyle | Optimize the style of plot
parse2GRanges | parse text into GRanges
parseWIG | convert WIG format track to BED format track
plotGRanges | plot GRanges data
plotIdeo | plot ideogram
plotOneIdeo | plot ideogram with data for one chromosome
pos | Class '"pos"'
pos-class | Class '"pos"'
reduce,GInteractions | Reduce method for 'GInteractions'
reduce-method | Reduce method for 'GInteractions'
renderbrowseTracks | Shiny bindings for browseTracks
seqlevels-method | Class '"trackStyle"'
seqlevelsStyle-method | Class '"trackStyle"'
seqlevelsStyle<--method | List of tracks
seqlevelsStyle<--method | Class '"trackStyle"'
setTrackStyleParam | Class '"trackStyle"'
setTrackStyleParam-method | Class '"trackStyle"'
setTrackViewerStyleParam | Class '"trackViewerStyle"'
setTrackViewerStyleParam-method | Class '"trackViewerStyle"'
setTrackXscaleParam | Class '"trackStyle"'
setTrackXscaleParam-method | Class '"trackStyle"'
setTrackYaxisParam | Class '"trackStyle"'
setTrackYaxisParam-method | Class '"trackStyle"'
show-method | Class '"trackStyle"'
track | Class '"trackStyle"'
track-class | Class '"trackStyle"'
trackList | List of tracks
trackList-class | List of tracks
trackStyle | Class '"trackStyle"'
trackStyle-class | Class '"trackStyle"'
trackViewer | Minimal designed plotting tool for genomic data
trackViewerStyle | Class '"trackViewerStyle"'
trackViewerStyle-class | Class '"trackViewerStyle"'
viewGene | plot tracks based on gene name
viewTracks | plot the tracks
xscale | Class '"xscale"'
xscale-class | Class '"xscale"'
yaxisStyle | Class '"yaxisStyle"'
yaxisStyle-class | Class '"yaxisStyle"'