• NNC (Nonparametric Nonlinear Correlation) - A Matlab toolbox for quantifying nonlinear correlation. Download the software as part of the supplements from our paper, Chen YA, Almeida JS, Richards AJ, Müller P, Carroll RJ, Rohrer B. A nonparametric approach to detect nonlinear correlation in gene expression. Journal of Computational and Graphical Statistics 2010, 19(3):552-568.


  • SinCHet: a MATLAB GUI toolbox for Single Cell Heterogeneity analysis in cancer. Bioinformatics 2017, 33(18):2951-2953. The SinCHet software is freely available for non-profit academic use.  You could download the source code here: or pre-compiled code here: SinCHet  Installation details are included in the SinCHet user manual here.



  • SinCHet-MS: A toolbox for analyzing single cell mass spectrometry (SCMS) heterogeneity. To be submitted.  The pre-compiled SinCHet-MS is available for download here.   


  • ISCVA: Interactive Single Cell Visual Analytics, a JavaScript-based tool for real-time animation of analytic algorithms for analyzing scRNA-seq in serial samples from cancer patients. (pronounced as Eye-VA, i.e., "SC" is silent), developed by Zhihua Chen. The manuscript describing ISCVA is currently under revision.  ISCVA has been used to analyze multiple scRNA-seq projects including a recent publication on identifying TME and sequential targeted and immuno-therapy for melanoma

 cancer patient single cell data