trackViewer

DOI: 10.18129/B9.bioc.trackViewer    

This package is for version 3.13 of Bioconductor; for the stable, up-to-date 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: 3.13

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>

Installation

To install this package, start R (version "4.1") and enter:

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

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")

 

HTML	R Script	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
PDF		Reference Manual
Text		NEWS

Details

biocViews	Software, Visualization
Version	1.28.1
In Bioconductor since	BioC 2.14 (R-3.1) (7.5 years)
License	GPL (>= 2)
Depends	R (>= 3.5.0), grDevices, methods, GenomicRanges, grid, Rcpp
Imports	GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, plotrix, Rgraphviz, InteractionSet, graph, utils, rhdf5
LinkingTo	Rcpp
Suggests	biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown
SystemRequirements
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_1.28.1.tar.gz
Windows Binary	trackViewer_1.28.1.zip
macOS 10.13 (High Sierra)	trackViewer_1.28.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/trackViewer
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/trackViewer
Package Short Url	https://bioconductor.org/packages/trackViewer/
Package Downloads Report	Download Stats