recoup

This is the released version of recoup; for the devel version, see recoup.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3

An R package for the creation of complex genomic profile plots

Bioconductor version: Release (3.23)

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")):

Panagiotis Moulos. recoup: An R package for the creation of complex genomic profile plots. doi:10.18129/B9.bioc.recoup, R package version 1.40.0, https://bioconductor.org/packages/recoup.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version	1.40.0
In Bioconductor since	BioC 3.3 (R-3.3) (10.5 years)
License	GPL (>= 3)
Depends	R (>= 4.0.0), GenomicRanges, GenomicAlignments, ggplot2, ComplexHeatmap
Imports	BiocGenerics, biomaRt, Biostrings, circlize, Seqinfo, GenomicFeatures, graphics, grDevices, httr, IRanges, methods, parallel, RSQLite, Rsamtools, rtracklayer, S4Vectors, stats, stringr, txdbmaker, utils
System Requirements
URL	https://github.com/pmoulos/recoup

Suggests	GenomeInfoDb, grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	recoup_1.40.0.tar.gz
Windows Binary (x86_64)	recoup_1.40.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	recoup_1.40.0.tgz
macOS Binary (sonoma-arm64)	recoup_1.40.0.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	https://bioconductor.org/packages/recoup/
Package Downloads Report	Download Stats