Computational Epigenetics & Bioinformatics

MOABS: MOdel based Analysis of Bisulfite Sequencing data

A complete, accurate and efficient solution for analysis of large scale base-resolution DNA methylation data, bisulfite sequencing or single molecule direct sequencing
We suggest MOABS on Bioconda at
Latest version of source code and mannual are available at

A hg38 reference genome contains lambda and virus genome: Link



LiBis: An ultrasensitive alignment method for low input bisulfite sequencing

LiBis is an integrated Python package for processing low input WGBS data such as cell-free DNA methylome and single-cell DNA methylome sequencing.

Latest version of source code and mannual are available at



GsmPlot: a web server to visualize epigenome data in NCBI

GsmPlot is a web service to automatically download, analyze and visualize epigenetics data (ChIP-Seq, ATAC-Seq, Bis-Seq), public from NCBI or private from you.



ExactNumCI: Exact Numerical Confidence Interval for binomial proportions

A package available in C++ and R library for exact numerical modeling of binomial proportions applicable to analysis of methylcytosine and hydroxymethycotine



MEPS: Methylation Pipeline and Service

A cloud computation solution for DNA methylation analysis to make it biologist friendly and as fast as coffee time



mSuite: DNA Methylation analysis in a Suite
It’s a packaging of ExactNumCI, MOABS, MEPS and other tools for analyzing DNA Methylation data.




Contributed Packages:


GenCat: Gene’s Comprehensive Annotation Tool

A New Gene Annotation tool using RNA-Seq data to discover New Gene with filtering of false positives, predicting coding potential and ORF, and integration with other knowledge.


RRBSMAP: Bisulfite Sequence Mapping Program

A short reads mapping software for bisulfite sequencing reads to study DNA cytosine methylation at single nucleotide resolution.