Lab GitHub page:


iTIME (interactive Tumor Immune MicroEnvironment) is a shiny application that creates interactive figures for examining spatial organization of individual tumors and provide basic spatial and summary information.


spatialTIME: R package for visualizing and analyzing multiplex Immunofluorescent (mIF) data for studying the tumor immune microenvironment (TIME).  


spatialGE: R package that provides visualizations and quantification of the tumor microenvironment heterogeneity through gene expression surfaces, spatial heterogeneity statistics that can be compared against clinical information, spot-level cell deconvolution and spatially informed clustering, all using a new data object to store data and resulting analyses simultaneously.


Pediatric Pharmacogenomics Regulome Explorer:  developed for chrome


NB.Mclust: R package for Negative binomial model-based clustering


IntNMF: R package for Integrative clustering of multiple genomic datasets with Non-negative matrix factorization (NMF). Approach was recently found to be the most powerful approach for integrated clustering by an independent research group (Cantini et al (2021) Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer. Nature Communication). 


InterSIM: R package for Simulation of Inter-Related Genomic Datasets. 


GMSimpute: R package for imputation of missing metabolite data using a 2-step LASSO approach.


PurBayes: R package for Bayesian estimation of tumor purity and clonality.


GSAgm: R package that completes a self-contained gene set analysis (GSA) for RNA-seq and SNP data using the Gamma Method.