RepViz

DOI: 10.18129/B9.bioc.RepViz    

Replicate oriented Visualization of a genomic region

Bioconductor version: Release (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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: