CoverageView

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see CoverageView.

Coverage visualization package for R

Bioconductor version: 3.8

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome

Author: Ernesto Lowy

Maintainer: Ernesto Lowy <ernestolowy at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:


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

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("CoverageView")

Easy visualization of the read coverage PDF R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ChIPSeq, ImmunoOncology, RNASeq, Sequencing, Software, Technology, Visualization

Version 1.20.1

In Bioconductor since BioC 2.14 (R-3.1) (10 years)

License Artistic-2.0

Depends R (>= 2.10), methods, Rsamtools(>= 1.19.17), rtracklayer

Imports S4Vectors(>= 0.7.21), IRanges(>= 2.3.23), GenomicRanges, GenomicAlignments, parallel, tools

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Package Archives

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

Source Package CoverageView_1.20.1.tar.gz

Windows Binary

Mac OS X 10.11 (El Capitan) CoverageView_1.20.1.tgz

Source Repository git clone https://git.bioconductor.org/packages/CoverageView

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CoverageView

Bioc Package Browser https://code.bioconductor.org/browse/CoverageView/

Package Short Url https://bioconductor.org/packages/CoverageView/

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Old Source Packages for BioC 3.8 Source Archive