• ISCVA (pronounced as Eye-VA, i.e., "SC" is silent), Interactive Single Cell Visual Analytics - a JavaScript-based visual analytics for analyzing scRNA-seq data:  The templates, functions and scripts are available here. The tool ISCVA has been used to analyze multiple scRNA-seq datasets including these published papers (Clin Cancer Res2021 and Cancer Immunology Research 2021), and a few others currently under review or in preparation.


  • 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  



  • 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.


  • 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


 cancer patient single cell data