extraChIPs
This is the development version of extraChIPs; for the stable release version, see extraChIPs.
All Bioconductor versions of extraChIPs
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15
Additional functions for working with ChIP-Seq data
Bioconductor version: 3.24 · Package version: 1.17.4
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 <stephen.pederson.au at gmail.com>
Citation
From within R, enter citation("extraChIPs"):
Stevie Pederson. extraChIPs: Additional functions for working with ChIP-Seq data. doi:10.18129/B9.bioc.extraChIPs, R package version 1.17.4, https://bioconductor.org/packages/extraChIPs.
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("extraChIPs")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.17.4 |
| License | GPL-3 |
| URL | https://github.com/smped/extraChIPs |
| Bug Reports | https://github.com/smped/extraChIPs/issues |
| Last updated | 2026-06-28 |
| In Bioconductor since | BioC 3.15 (R-4.2) (4 years) |
| Downloads rank | 1050 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ChIPSeq, Coverage, HiC, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/extraChIPs/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("extraChIPs")| extraChIPs: Differential Signal Using Fixed-Width Windows | HTML | R Script |
| extraChIPs: Differential Signal Using Sliding Windows | HTML | R Script |
| extraChIPs: Range-Based operations | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | extraChIPs_1.17.4.tar.gz |
| macOS binary (arm64) | extraChIPs_1.17.4.tgz |
| macOS binary (x86_64) | extraChIPs_1.17.4.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/extraChIPs |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/extraChIPs |
| Package Downloads Report | Download Stats |
Dependencies
Depends: BiocParallel, R (>= 4.2.0), GenomicRanges, ggplot2 (>= 4.0.0), ggside (>= 0.4.0), Seqinfo, SummarizedExperiment (>= 1.39.1), tibble
Imports: csaw, dplyr (>= 1.1.1), edgeR (>= 4.0), forcats, GenomeInfoDb, glue, ggrepel, InteractionSet, IRanges, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, vctrs
Suggests: apeglm, BiocStyle, SimpleUpset, covr, DESeq2, EnrichedHeatmap, GenomicAlignments, GenomicInteractions, Gviz, ggforce, harmonicmeanp, here, knitr, limma, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse, VennDiagram
Reverse dependencies
Suggests Me (2): motifTestR, transmogR