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)
These are tools for post GWAS analysis. Please see below link as a document for install and use.
Find Prokaryotic DNA methylase genes in proteins, contigs, or genomes
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.
ATAC-seq Processing Engine
cccTeqy is a ChIP-seq, CUT&RUN, and CUT&Tag processing engine.
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