trackViewer

This is the development version of trackViewer; for the stable release version, see trackViewer.

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

Bioconductor version: Development (3.18)

Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.

Author: Jianhong Ou [aut, cre] , Julie Lihua Zhu [aut]

Maintainer: Jianhong Ou <jianhong.ou at duke.edu>

Citation (from within R, enter citation("trackViewer")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("trackViewer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("trackViewer")

trackViewer Vignette: change the track styles	HTML	R Script
trackViewer Vignette: dandelionPlot	HTML	R Script
trackViewer Vignette: lollipopPlot	HTML	R Script
trackViewer Vignette: overview	HTML	R Script
trackViewer Vignette: plot interaction data	HTML	R Script
Reference Manual	PDF
NEWS	Text

Details

biocViews	Software, Visualization
Version	1.37.14
In Bioconductor since	BioC 2.14 (R-3.1) (9.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), grDevices, methods, GenomicRanges, grid
Imports	GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils, rhdf5, strawr
Linking To
Suggests	biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack
System Requirements
Enhances
URL

Depends On Me
Imports Me	NADfinder
Suggests Me	ATACseqQC, ChIPpeakAnno
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	trackViewer_1.37.14.tar.gz
Windows Binary	trackViewer_1.37.14.zip
macOS Binary (x86_64)	trackViewer_1.37.14.tgz
macOS Binary (arm64)	trackViewer_1.37.14.tgz
Source Repository	git clone https://git.bioconductor.org/packages/trackViewer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/trackViewer
Bioc Package Browser	https://code.bioconductor.org/browse/trackViewer/
Package Short Url	https://bioconductor.org/packages/trackViewer/
Package Downloads Report	Download Stats