HicAggR

HicAggR provides functions for the analysis of 3D genomic interactions, including import of standard HiC data formats into R, HiC normalisation procedures, and aggregation-based visualization and quantification of HiC contacts.

Key Features:

• HiC Data Import: Imports standard HiC data formats into R.
• HiC Normalisation: Includes HiC normalisation procedures.
• 1D Genomics Data Integration: Imports 1D genomics data such as peaks from ATACSeq and ChIPSeq.
• Feature Pair Generation: Creates potential couples between features of interest under user-defined parameters such as distance between pairs of features of interest.
• Contact Value Extraction: Extracts contact values from HiC data for generated feature couples.
• Aggregated Peak Analysis: Performs Aggregated Peak Analysis (APA) for visualization.
• Condition Comparison: Compares normalized contact values between conditions.

Scientific Applications:

• 3D Genomic Interaction Analysis: Analyzes 3D genomic interactions through aggregation-based approaches.
• Integration of 1D and 3D Genomics Data: Integrates 1D genomics data with 3D genomics data to provide access to HiC contact values.
• Visualization of HiC Contacts: Improves visualization of HiC contacts through Aggregated Peak Analysis.
• Quantitative Comparison of Chromatin Interactions: Compares normalized contact values between experimental conditions.

Methodology:

The package imports standard HiC data formats into R, applies HiC normalisation procedures, imports 1D genomics data such as peaks from ATACSeq and ChIPSeq, creates potential couples between features of interest under user-defined parameters, extracts contact values from HiC data for these couples, and performs Aggregated Peak Analysis for visualization and comparison of normalized contact values between conditions.