extraChIPs: Detection and Visualisation of Differential ChIP-Seq Signal

extraChIPs: Detection and Visualisation of Differential ChIP-Seq Signal

Author(s): Stevie M Pederson

Affiliation(s): Telethon Kids Institute, Adelaide, Australia

Designed as core infrastructure for the larger “Gene Regulatory Analysis using Variable Inputs” (GRAVI) workflow (https://github.com/steveped/GRAVI), extraChIPs enables differential Chip-Seq Signal analysis using either fixed width ranges or sliding windows, in a peak-dependent or peak-agnostic manner. Merging strategies for sliding window analysis build on those provided in csaw with the addition of the harmonic mean p-value for combining dependent test results. All range-focussed functions are designed to operate in a tidy-friendly manner, with a strong focus on data in the mcols element as well as the GRanges backbone. Integration with peak-callers, such as macs2, is implemented along with easy and flexible identification of consensus peaks and enabling cross-sample comparisons. With a clear focus on enabling data integration, mapping of ranges to genes is performed by incorporating genomic annotations and 3D conformational information, such as that provided by HiC experiments. Core visualisations (RLE, PCA and Density plots) are enabled for SummarizedExperiment objects, as well as robust implementation of multi-factor Pie and Split-level Donut plots for visualisation of range distributions and results. Functions for generation of profile heatmaps across multiple ranges are provided, as are convenience functions for comparing HiC, Genomic Features, Genes and Coverage across multiple ranges.

Source code

On YouTube: