Bioconductor Packages

CHiCAGO: Capture Hi-C Analysis of Genomic Organization

Binomial test for Hi-C data analysis

A R/Bioconductor package to detect the interaction nodes from HiC/HiChIP/HiCAR data

Framework for Storing and Accessing Hi-C Data Through HDF Files

Hi-C Direct Caller Plus

A/B compartment detection and differential analysis

Bioconductor class for interacting with Hi-C files in R

Parser for HiC data in R

HiCaptuRe: Manipulating and integrating Capture Hi-C data

HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets

Analysing cool files in R with HiContacts

HiCool

Hierarchical Inference of Spatial Positions from Hi-C Data

High Throughput Chromosome Conformation Capture analysis

Set of 3D genomic interaction analysis tools

Search for correlation between epigenetic signals and gene expression in TADs

Base Classes for Storing Genomic Interaction Data

3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

SpectralTAD: Hierarchical TAD detection using spectral clustering

TADCompare: Identification and characterization of differential TADs

Bandwise normalization and batch correction of Hi-C data

Differential Analysis of Hi-C Data

Additional functions for working with ChIP-Seq data

Venn Diagram for genomic interaction data

Irreproducible Discovery Rate for Genomic Interactions Data

Base Classes for Storing Genomic Link Data

Mariner: Explore the Hi-Cs

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Coordinate-Based Genomic Visualization Package for R

preciseTAD: A machine learning framework for precise TAD boundary prediction

Integerated visualization of epigenomic data

Differential Analysis of Single-cell Hi-C Data

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Identification of enriched motif pairs from chromatin interaction data