Software

  • 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: SinCHet_source_code.zip or pre-compiled code here: SinCHet Compiled.zip.  Installation details are included in the SinCHet user manual here.

 

  • GMSImpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis.  Our manuscript is accepted for publication, and to appear in Bioinformatics soon in 2019.  The R package is available at CRAN: https://cran.r-project.org/web/packages/GMSimpute/index.html

 

  • 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.   

 

  • SCIVA: Single Cell Interactive 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 Sy-Va, similar to how Sci-Fi is pronounced for Science Fiction, but no fiction here). Currently under development by Zhihua Chen.

 cancer patient single cell data