Software

We currently develop and maintain tools for three major areas. 

Single Cell
​Genomics

Citrus
Removing unwanted variation using Spike-ins

VIPER
Variability-preserving imputation for single-cell RNA-seq

dmatch
Alignment of single-cell RNA-seq samples using density matching

HIPPO 
Heterogeneity inspired pre-processing

Epigenomics &
Epitranscriptomics

RADAR 
​Differential methylation analysis for m6A sequence data

​REPIC
A database for Epitranscriptomics

easym6A
A pipeline for m6A sequencing data pre-processing

​eTAM-seq workflow
A workflow for eTAM-seq data processing

Cancer
​Genomics

SynthEx
A comprehensive suite of tools for CNA detection and tumor heterogeneity profiling

Check our github page for more information: 
​https://github.com/chenmengjie 

The list of old software without maintenance or updates (as it is when published):

• ANTAC: asymptotic normal estimation of covariate-adjusted gaussian graphical models. [Source] 
• DepthDescent: compute matrix depth using a greed search strategy. [Github]
• SomatiCA: Identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing [Bioconductor] 
  
• BCP-mixture: A Bayesian change point method for epigenetic block identification [Source] 
• MBAmethyl: Model-based analysis of DNA methylation data [Bioconductor]