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This is the development version of recoup; for the stable release version, see recoup.

An R package for the creation of complex genomic profile plots

Bioconductor version: Development (3.20)

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>

Maintainer: Panagiotis Moulos <moulos at>

Citation (from within R, enter citation("recoup")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the recoup package HTML R Script
Reference Manual PDF


biocViews ATACSeq, Alignment, ChIPSeq, ChipOnChip, Coverage, DataImport, GeneExpression, ImmunoOncology, Preprocessing, QualityControl, RNASeq, Sequencing, Software
Version 1.33.0
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, txdbmaker, utils
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Suggests grid, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RMySQL
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Follow Installation instructions to use this package in your R session.

Source Package recoup_1.33.0.tar.gz
Windows Binary
macOS Binary (x86_64) recoup_1.33.0.tgz
macOS Binary (arm64) recoup_1.33.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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