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extraChIPs

Additional functions for working with ChIP-Seq data


Bioconductor version: Release (3.18)

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 included.

Author: Stephen Pederson [aut, cre]

Maintainer: Stephen Pederson <stephen.pederson.au at gmail.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("extraChIPs")

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("extraChIPs")
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
NEWS Text

Details

biocViews ChIPSeq, Coverage, HiC, Sequencing, Software
Version 1.6.1
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 (>= 0.3.0), SummarizedExperiment, tibble
Imports BiocIO, broom, ComplexUpset, csaw, dplyr (>= 1.1.1), edgeR, EnrichedHeatmap, forcats, GenomeInfoDb, GenomicInteractions, ggforce, ggrepel, glue, grDevices, grid, Gviz, InteractionSet, IRanges, limma, matrixStats, methods, patchwork, RColorBrewer, rlang, Rsamtools, rtracklayer, S4Vectors, scales, stats, stringr, tidyr, tidyselect, utils, vctrs, VennDiagram
System Requirements
URL https://github.com/smped/extraChIPs
Bug Reports https://github.com/smped/extraChIPs/issues
See More
Suggests BiocStyle, covr, cqn, harmonicmeanp, here, knitr, magrittr, plyranges, quantro, rmarkdown, testthat (>= 3.0.0), tidyverse
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Package Archives

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

Source Package extraChIPs_1.6.1.tar.gz
Windows Binary extraChIPs_1.6.1.zip (64-bit only)
macOS Binary (x86_64) extraChIPs_1.6.1.tgz
macOS Binary (arm64) extraChIPs_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/extraChIPs
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/extraChIPs
Bioc Package Browser https://code.bioconductor.org/browse/extraChIPs/
Package Short Url https://bioconductor.org/packages/extraChIPs/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive