RepViz
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see RepViz.
Replicate oriented Visualization of a genomic region
Bioconductor version: 3.10
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("RepViz")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("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")| RepViz | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, ChIPSeq, Coverage, GenomicVariation, Sequencing, Software, Visualization, WorkflowStep |
| Version | 1.2.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| 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 | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RepViz_1.2.0.tar.gz |
| Windows Binary | RepViz_1.2.0.zip |
| Mac OS X 10.11 (El Capitan) | RepViz_1.2.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RepViz |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RepViz |
| Bioc Package Browser | https://code.bioconductor.org/browse/RepViz/ |
| Package Short Url | https://bioconductor.org/packages/RepViz/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |