- SinCHet-MS: A MATLAB toolbox for analyzing single cell mass spectrometry (SCMS) heterogeneity. To be submitted. The pre-compiled SinCHet-MS is available for download here. The User manual could be download here and source files here.
- DRepMel, a multiomics drug repurposing approach with a Shiny app, predicts combination therapies for melanoma patients by integrating exome sequencing, RNA-seq data, clinical outcomes and potential functional impact (using eQTL analysis) in two large independent melanoma patient cohorts. This also provides the potential impact on TME using scRNA-seq data from 28K cells from melanoma patients. The user manual could be downloaded here.
- GMSImpute: a generalized two-step Lasso approach to impute missing values in label-free mass spectrum analysis. Bioinformatics. 2020;. doi: 10.1093/bioinformatics/btz488. The R package is available at CRAN: https://cran.r-project.org/web/packages/GMSimpute/index.html
- 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.
- 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