🎯 ChIP peak Annotation, Comparison and Visualization

• UpdatedFeb 4, 2025
• R

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

• UpdatedMar 16, 2025
• Nextflow

Multiome GRN inference.

• UpdatedApr 19, 2024
• R

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

• UpdatedDec 14, 2022
• Jupyter Notebook

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

• UpdatedJun 21, 2022
• HTML

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

• UpdatedMay 16, 2023
• Rust

Methods for summarizing and visualizing multi-biosample functional genomic annotations

• UpdatedAug 31, 2023
• Python

Toolkit for single-cell DNA methylation analysis.

• UpdatedMar 3, 2025
• Python

Python package to analyze DNA methylation data

• UpdatedNov 15, 2024
• Python

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

• UpdatedAug 16, 2023
• Python

Bead-based single-cell atac processing

• UpdatedNov 13, 2021
• Python

Predicting regulatory DNA elements based on epigenomic signatures

• UpdatedJun 26, 2024
• Python

Molecular interactions inference from single-cell multi-omics data

• UpdatedNov 6, 2024
• R

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

• UpdatedMar 12, 2025
• Python

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

• UpdatedMay 22, 2023
• Python

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

• UpdatedMay 2, 2022
• C

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

• UpdatedJul 7, 2023
• R

Application for semi-automated genomic annotation.

• UpdatedJul 12, 2024
• Shell

ChromSCape

• UpdatedJan 22, 2024
• R

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

• UpdatedAug 19, 2020
• Shell