Methylation (Bisulfite-Sequencing) analysis pipeline using Bismark/bwa-meth + MethylDackel or bwa-mem + rastair
CUT&RUN and CUT&Tag data processing and analysis
WashU Epigenome Browser (3rd generation, since 2025)
Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes
These are tools for post GWAS analysis. Please see below link as a document for install and use.
A unified framework for discovering, analyzing, integrating, and visualizing regulatory motifs and transcription factor binding sites across bulk, single-cell, and long-read sequencing modalities.
Pipeline for Sequential Analysis of MacroMolecules accessibilitY sequencing (SAMMY-seq) data, to analyze chromatin state.
Perl, R, Python, and Bash Shell source codes for high-throughput sequencing (the 2nd, 3rd, and 4th generation sequencing for DNA, RNA, and Protein) data analysis by integrating lots of open-source tools or softwares.
An R package for weighted region comethylation network analysis
An nf-core pipeline for epigenome segmentation using EpiSegMix/Meth — a hidden Markov model with flexible read count distributions and state duration modeling for histone, open chromatin, and methylation signals.
This is the analysis for the Babies GROWELL Project
Following Horvath epigenetic clock published in 2013, using SHAP to select top 100 CpG loci, with SHAP not just the final interpretation
This is the Repo for the GROWELL Comethyl project
This is the analysis for the CHDS Intergenerational Breast Cancer Project
Bulk ATAC-seq Snakemake workflow: Compatible with local and LSF-based HPC systems
Cancer is calculable, geometric attractor framework. This is an OrganismCore derivative framework.
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