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Additional functions for working with ChIP-Seq data

Bioconductor version: Release (3.19)

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))


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 1.8.1
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
Linking To
Depends On Me
Imports Me
Suggests Me motifTestR, transmogR
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Package Archives

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

Source Package extraChIPs_1.8.1.tar.gz
Windows Binary
macOS Binary (x86_64) extraChIPs_1.8.1.tgz
macOS Binary (arm64) extraChIPs_1.8.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive