HiCDCPlus

HiCDCPlus enables principled statistical analysis of Hi-C and HiChIP data sets, including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments, to facilitate global integrative studies.

Key Features:

• Significant interaction calling: Estimates significant interactions directly from the raw contact matrix for each chromosome up to a specified genomic distance.
• Flexible binning: Supports binning by uniform genomic intervals or restriction enzyme fragments.
• Background model training: Trains a background model to account for random polymer ligation and systematic sources of read count variation.
• Differential analysis: Performs differential analysis between conditions given replicate experiments.

Scientific Applications:

• Hi-C data analysis: Enables systematic 3D interaction calls for Hi-C experiments.
• HiChIP data analysis: Enables systematic 3D interaction calls for HiChIP experiments.
• Global integrative studies: Facilitates integrative analysis of chromatin interaction data across conditions.

Methodology:

HiCDCPlus estimates significant interactions by training a background model to account for random polymer ligation and systematic sources of read count variation.