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

Additional functions for working with ChIP-Seq data

Bioconductor version: Development (3.20)

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

Author: Stevie Pederson [aut, cre]

Maintainer: Stevie Pederson < at>

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


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:

Differential Signal Analysis (Fixed-Width Windows) HTML R Script
Differential Signal Analysis (Sliding Windows) HTML R Script
Range-Based Operations HTML R Script
Reference Manual PDF


biocViews ChIPSeq, Coverage, HiC, Sequencing, Software
Version 1.9.1
In Bioconductor since BioC 3.15 (R-4.2) (2 years)
License GPL-3
Depends BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 3.5.0), ggside (>= 0.3.1), SummarizedExperiment, tibble
Imports BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR(>= 4.0), forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram
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Suggests BiocStyle, covr, cqn, DESeq2, EnrichedHeatmap, Gviz, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse
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Follow Installation instructions to use this package in your R session.

Source Package extraChIPs_1.9.1.tar.gz
Windows Binary
macOS Binary (x86_64) extraChIPs_1.9.1.tgz
macOS Binary (arm64) extraChIPs_1.9.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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