- shinyGEO : an online tool for identifying biomarkers in Gene Expression Omnibus (GEO) datasets. PMID: 27503226
- swirl-tbp : a package for interactively learning R programming and data science through the addition of 'template-based practice problems' in swirl. (useR! 2016 abstract)
- Bladder Cancer Biomarker Evaluation Tool : Evaluation of candidate biomarkers in bladder cancer based on gene expression data. PMID: 26126604.
- CCM: CCM is an R package that implements a Correlation Classification Method that classifies a test sample according to its mean correlation with all training samples having known classes. This is a robust and accurate method for predicting tissue of origin and bladder cancer stage from gene expression data. PMID: 22012889.
- mlegp : Gaussian processes (GPs) are a common class of surrogate statistical models for predicting the output of non-linear and high-dimensional computer simulations. The R package mlegp incorporates maximum likelihood estimates for Gaussian processes to model univariate and multi-dimensional outputs
A version of mlegp that implements sensitivity analysis is also available by request. We have found mlegp useful for calibrating and analyzing an agent-based model of Leishmania major infection. PMID: 18635570.
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