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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: Release (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")

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 1.38.1
In Bioconductor since BioC 2.14 (R-3.1) (10 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
System Requirements
URL
See More
Suggests biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation, httr, htmltools, rmarkdown, motifStack
Linking To
Enhances
Depends On Me
Imports Me NADfinder
Suggests Me ATACseqQC, ChIPpeakAnno
Links To Me
Build Report Build Report

Package Archives

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

Source Package trackViewer_1.38.1.tar.gz
Windows Binary trackViewer_1.38.1.zip
macOS Binary (x86_64) trackViewer_1.38.1.tgz
macOS Binary (arm64) trackViewer_1.38.1.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
Old Source Packages for BioC 3.18 Source Archive