🎯 ChIP peak Annotation, Comparison and Visualization

Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark or bwa-meth + MethylDackel

Multiome GRN inference.

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

☄️ Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)

Methods for summarizing and visualizing multi-biosample functional genomic annotations

Toolkit for single-cell DNA methylation analysis.

Python package to analyze DNA methylation data

The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)

Bead-based single-cell atac processing

Predicting regulatory DNA elements based on epigenomic signatures

Molecular interactions inference from single-cell multi-omics data

Genepy is an open source utils package covering a range of useful functions for large scale genomics data analysis in python

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Suite of command-line software for high-performance graphical analysis of ChIP-seq/RNA-seq/ATAC-seq data

FinaleToolkit is a package and standalone program to extract fragmentation features of cell-free DNA from paired-end sequencing data.

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

ChromSCape

BioMM: Biological-informed Multi-stage Machine learning framework for phenotype prediction using omics data