Bioinformatics and related tools

• CPP: a Cancer Publication Portal for summarizing and searching cancer genomic publications [F1000 Publication: 8-2073; AACR abstracts: 2019, 2018]

• shinyGEO: an online tool for identifying biomarkers in Gene Expression Omnibus (GEO) datasets [PMID: 27503226]

• Bladder Cancer Biomarker Evaluation Tool: Evaluation of candidate biomarkers in bladder cancer based on gene expression data [PMID: 26126604]

• Bladder Cancer Methyl Biomarker Evaluation Tool: A database for evaluation of methylation biomarkers in bladder cancer [AACR 2017]

• 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 [Manual]. 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].

Educational tools

Additional tools

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