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Software

We currently develop and maintain tools for three major areas. 
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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
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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
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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]

Location

Chen Group

Section of Genetic Medicine
​University of Chicago​
5841 S. Maryland Ave N417A
Chicago, IL 60637 USA
Tel: 773-834-3175 
Email: [email protected]

Funded by

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