recoup

DOI: 10.18129/B9.bioc.recoup    

This package is for version 3.13 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: 3.13

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 (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("recoup")

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("recoup")

 

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

Details

biocViews	ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	1.20.1
In Bioconductor since	BioC 3.3 (R-3.3) (5.5 years)
License	GPL (>= 3)
Depends	R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports	BiocGenerics, biomaRt, Biostrings, circlize, GenomeInfoDb, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, utils
LinkingTo
Suggests	grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL
SystemRequirements
Enhances
URL	https://github.com/pmoulos/recoup
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	recoup_1.20.1.tar.gz
Windows Binary	recoup_1.20.1.zip
macOS 10.13 (High Sierra)	recoup_1.20.1.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	https://bioconductor.org/packages/recoup/
Package Downloads Report	Download Stats