epigenomics

🎯 ChIP peak Annotation, Comparison and Visualization

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

Multiome GRN inference.

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

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

Toolkit for single-cell DNA methylation analysis.

Methods for summarizing and visualizing multi-biosample functional genomic annotations

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Python package to analyze DNA methylation data

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

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

Bead-based single-cell atac processing

Molecular interactions inference from single-cell multi-omics data

Predicting regulatory DNA elements based on epigenomic signatures

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

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

Application for semi-automated genomic annotation.

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Data processing and analysis workflow for GAGE-seq, a coassay of single-cell HiC and single-cell RNA-seq

rvDNA — AI-native genomic analysis in pure Rust + WASM: biomarker risk scoring, 23andMe genotyping, CYP2D6/CYP2C19 pharmacogenomics, variant calling, protein prediction, epigenomics, and HNSW vector search.