extraChIPs

extraChIPs extends existing ChIP-Seq analysis capabilities by adding functions for detecting differential binding windows/regions, performing set-operations on GRanges objects while retaining mcols, and aiding visualisation of results.

Key Features:

• Set-operations for GRanges: Performs set-operations on GRanges objects whilst retaining mcols metadata columns.
• Differential binding detection: Provides functions focused on detecting differential binding windows/regions in ChIP-Seq data.
• Visualisation support: Includes functions to aid visualisation of ChIP-Seq analysis results.
• Tibble coercion: Implements coercion of objects to tibble format for downstream data manipulation.

Scientific Applications:

• ChIP-Seq differential binding analysis: Enables detection of differential binding windows and regions in ChIP-Seq experiments.
• Genomic range manipulation: Facilitates set-operations on GRanges objects with preservation of metadata for genomic interval analysis.

Methodology:

The package builds on existing tools and adds capabilities for working with ChIP-Seq data, with functions for set-operations on GRanges objects, differential binding detection, visualisation, and coercion to tibble objects.