To install this package, start R and enter:

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

In most cases, you don't need to download the package archive at all.

recoup

This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see recoup.

An R package for the creation of complex genomic profile plots

Bioconductor version: 3.4

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

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

Details

biocViews ChIPSeq, Coverage, GeneExpression, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL (>= 3)
Depends GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports BiocGenerics, biomaRt, circlize, rtracklayer, plyr
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.

Package Source recoup_1.2.0.tar.gz
Windows Binary recoup_1.2.0.zip
Mac OS X 10.9 (Mavericks) recoup_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/recoup/tree/release-3.4
Package Short Url http://bioconductor.org/packages/recoup/
Package Downloads Report Download Stats

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