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

https://s3.amazonaws.com/deqiangsun/software/moabs/moabs-v1.3.4.src.x86_64_Linux.data.tar.gz
We suggest MOABS on Bioconda at https://anaconda.org/bioconda/moabs
Latest version of source code and mannual are available at https://github.com/sunnyisgalaxy/moabs

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 https://github.com/Dangertrip/LiBis

 

 

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.

https://gsmplot.deqiangsun.org/

 

 

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. 

http://code.google.com/p/gencat/

 

RRBSMAP: Bisulfite Sequence Mapping Program

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

http://code.google.com/p/bsmap/