RepViz

DOI: 10.18129/B9.bioc.RepViz    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see RepViz.

Replicate oriented Visualization of a genomic region

Bioconductor version: 3.9

RepViz enables the view of a genomic region in a simple and efficient way. RepViz allows simultaneous viewing of both intra- and intergroup variation in sequencing counts of the studied conditions, as well as their comparison to the output features (e.g. identified peaks) from user selected data analysis methods.The RepViz tool is primarily designed for chromatin data such as ChIP-seq and ATAC-seq, but can also be used with other sequencing data such as RNA-seq, or combinations of different types of genomic data.

Author: Thomas Faux, Kalle Rytkönen, Asta Laiho, Laura L. Elo

Maintainer: Thomas Faux, Asta Laiho <faux.thomas1 at gmail.com> <asta.laiho at utu.fi>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("RepViz")

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("RepViz")

 

HTML	R Script	RepViz
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, ChIPSeq, Coverage, GenomicVariation, Sequencing, Software, Visualization, WorkflowStep
Version	1.0.0
In Bioconductor since	BioC 3.9 (R-3.6) (< 6 months)
License	GPL-3
Depends	R (>= 3.5.1), GenomicRanges(>= 1.30.0), Rsamtools(>= 1.34.1), IRanges(>= 2.14.0), biomaRt(>= 2.36.0), S4Vectors(>= 0.18.0), graphics, grDevices, utils
Imports
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	RepViz_1.0.0.tar.gz
Windows Binary	RepViz_1.0.0.zip
Mac OS X 10.11 (El Capitan)	RepViz_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/RepViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/RepViz
Package Short Url	https://bioconductor.org/packages/RepViz/
Package Downloads Report	Download Stats