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 |
| 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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