# extraChIPs <img id="extrachips_logo" src="man/figures/extraChIPs.png" align="right" width = "125" /> <!-- badges: start --> [![Build Status](https://github.com/smped/extraChIPs/workflows/R-CMD-check-bioc/badge.svg)](https://github.com/smped/extraChIPs/actions) [![Codecov test coverage](https://codecov.io/gh/smped/extraChIPs/branch/main/graph/badge.svg)](https://codecov.io/gh/smped/extraChIPs?branch=main) [![Repo Status](https://img.shields.io/badge/repo%20status-Active-green.svg)](https://shields.io/) <!-- badges: end --> `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](https://github.com/smped/GRAVI) 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`. ```r install.packages("BiocManager") BiocManager::install("extraChIPs") ``` To install the development version from github ```r BiocManager::install("smped/extraChIPs") ```