idr2d

idr2d extends the Irreproducible Discovery Rate (IDR) method to identify reproducible two-dimensional genomic interactions from chromatin interaction experiments such as ChIA-PET, HiChIP, and Hi-C.

Key Features:

• Two-dimensional IDR extension: Adapts the original one-dimensional IDR framework to analyze interactions between peaks rather than individual peaks.
• Replicable interaction detection: Identifies shared interactions across replicate chromatin interaction experiments while eliminating artifacts from single experiments.
• Bioconductor integration: Available as an R package for the Bioconductor community.

Scientific Applications:

• Chromatin interaction quality control: Distinguishes true biological interactions from spurious ones in ChIA-PET, HiChIP, and Hi-C data.
• Genome organization analysis: Provides a principled set of reproducible interactions for studying genome organization and gene regulation.

Methodology:

IDR2D extends the original idr package, which was developed for one-dimensional ChIP-seq peaks, to handle two-dimensional peaks representing genomic interactions.