recoup

DOI: 10.18129/B9.bioc.recoup    

This is the development version of recoup; for the stable release version, see recoup.

An R package for the creation of complex genomic profile plots

Bioconductor version: Development (3.8)

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Author: Panagiotis Moulos <moulos at fleming.gr>

Maintainer: Panagiotis Moulos <moulos at fleming.gr>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("recoup")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("recoup")

 

HTML R Script Introduction to the recoup package
PDF   Reference Manual
Text   NEWS

Details

biocViews ChIPSeq, Coverage, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.9.0
In Bioconductor since BioC 3.3 (R-3.3) (2 years)
License GPL (>= 3)
Depends R (>= 2.13.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports BiocGenerics, biomaRt, circlize, graphics, grDevices, methods, rtracklayer, plyr, stats, utils
LinkingTo
Suggests grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocInstaller, BSgenome, RSQLite, RMySQL
SystemRequirements
Enhances parallel
URL https://github.com/pmoulos/recoup
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package recoup_1.9.0.tar.gz
Windows Binary recoup_1.9.0.zip
Mac OS X 10.11 (El Capitan) recoup_1.9.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/recoup
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recoup
Package Short Url http://bioconductor.org/packages/recoup/
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