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recoup

An R package for the creation of complex genomic profile plots


Bioconductor version: Release (3.18)

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 (version "4.3") 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

Details

biocViews ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL https://github.com/pmoulos/recoup
See More
Suggests grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL
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Package Archives

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

Source Package recoup_1.30.0.tar.gz
Windows Binary recoup_1.30.0.zip
macOS Binary (x86_64) recoup_1.30.0.tgz
macOS Binary (arm64) recoup_1.30.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/recoup
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/recoup
Bioc Package Browser https://code.bioconductor.org/browse/recoup/
Package Short Url https://bioconductor.org/packages/recoup/
Package Downloads Report Download Stats