Lab GitHub page: https://github.com/FridleyLab

 

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. http://itime.moffitt.org/

 

spatialTIME: R package for visualizing and analyzing multiplex Immunofluorescent (mIF) data for studying the tumor immune microenvironment (TIME).  https://cran.r-project.org/package=spatialTIME  

 

Pediatric Pharmacogenomics Regulome Explorer:  developed for chrome   http://explorerpedpgx.moffitt.org/landing

 

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

 

https://CRAN.R-project.org/package=NB.MClust

 

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).

https://CRAN.R-project.org/package=IntNMF 

 

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

 https://CRAN.R-project.org/package=InterSIM 

 

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

https://CRAN.R-project.org/package=GMSimpute

 

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

https://CRAN.R-project.org/package=PurBayes

 

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

https://CRAN.R-project.org/package=GSAgm