Accurate and flexible loops calling tool for 3D genomic data.

Enhanced and elegant flexible peak/loop/domain -calling and analysis tool for 1D/3D genomic data.

A preprocessing and QC pipeline for HiChIP data

LoopPredictor: Predicting unknown enhancer-mediated genome topology by an ensemble machine learning model

Scripts to create cartoons of 3D genomes

7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Bioinformatic analysis of RNA-Seq, WGBS, and Hi-C in Arabidopsis

An R package for analyzing UMI-4C chromatin contact data.

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

Identification of dynamic changes in chromatin conformation is a fundamental task in genetics. In 2020, Galan et al. presented CHESS (Comparison of Hi-C Experiments using Structural Similarity), a novel computational algorithm designed for systematic identification of structural differences in chromatin-contact maps. Using CHESS, the same group …

Code for my Master project

RB represses cohesin-dependent loop formation and safeguards E2F-independent transcription

Statistical Modeling of ChIA-PET interactions

HiSIF: Genome-wide chromatin interactions identify characteristic promoter-distal loops