extraChIPs

extraChIPs is a package primarily designed to enable ChIP-Seq analysis. Whilst the package was primarily built for the GRAVI: Gene Regulatory Analysis using Variable Inputs
workflow, the functionality extends beyond this specific application. Functions focus primarily on

• Retaining mcols() when manipulating GRanges objects
• Common visualisation utilities for ChIP-Seq analysis
• Enabling sliding window analysis for differential ChIP-target binding

It is intended that these functions will integrate seamlessly with other packages such as those provided in csaw, plyranges and limma.

In addition to enabling workflows, simple coercion to tibble objects from DataFrame, GRanges and GInteractions objects is implemented.

Installation Instructions

To install this package from Bioconductor, please use BiocManager.

install.packages("BiocManager")
BiocManager::install("extraChIPs")

To install the development version from github

BiocManager::install("smped/extraChIPs")