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trackViewer (development version)

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

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DOI: 10.18129/B9.bioc.trackViewer

Bioconductor version: Development (3.23)

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] ORCID iD ORCID: 0000-0002-8652-2488 , Julie Lihua Zhu [aut]

Maintainer: Jianhong Ou <jou at morgridge.org>

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

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Software, Visualization

Version 1.47.0

In Bioconductor since BioC 2.14 (R-3.1) (11.5 years)

License GPL (>= 2)

Depends R (>= 3.5.0), grDevices, methods, GenomicRanges, grid

Imports Seqinfo, GenomeInfoDb, GenomicAlignments, GenomicFeatures, Gviz, Rsamtools, S4Vectors, rtracklayer, BiocGenerics, scales, tools, IRanges, AnnotationDbi, grImport, htmlwidgets, InteractionSet, utils, rhdf5, strawr, txdbmaker

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 geomeTriD, 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_1.47.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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/

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