recoup

DOI: 10.18129/B9.bioc.recoup    

An R package for the creation of complex genomic profile plots

Bioconductor version: Release (3.6)

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>

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

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

Details

biocViews	ChIPSeq, Coverage, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	GPL (>= 3)
Depends	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_1.6.0.tar.gz
Windows Binary	recoup_1.6.0.zip
Mac OS X 10.11 (El Capitan)	recoup_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/recoup
Package Short Url	http://bioconductor.org/packages/recoup/
Package Downloads Report	Download Stats