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BB SRF Specialized Software Tools

  • An R package ordcrm developed by Emily Van Meter provides the setup and calculations needed to design and implement a likelihood-based, continual reassessment method (CRM) dose-finding trial incorporating either binary or ordinal toxicities. Additionally, this package can perform simulations to assess design performance under various criteria. Documentation files and functions are described in more detail here.
  • BEAU is an R package developed by Dr. Chi Wang for implementing a Bayesian approach to estimate the effect on the outcome associated with an exposure of interest while accounting for the uncertainty in the confounding adjustment. More information can be found here
  • Dr. Jinze Liu has developed multiple functions for bioinformatics applications in R. These include Software for Alignment: MapSplice, MapPER and software for differential transcriptome analysis: FDM. Please email Dr. Liu for more information at

BB SRF Personnel Statistical Software Expertise

Our faculty and staff have extensive experience and expertise with many statistical software packages to help develop studies, calculate sample sizes with adequate power, and perform data analyses for MCC investigators across all Cancer Center research programs. We are happy to collaborate with researchers on a project that may require specialized software. Our statistical package experience includes (but is not limited to):

  • General Purpose: SAS, SUDANN, SPSS, MINITAB, StatXact, LogXact, STATA
  • Design and Sample Size: nQuery Advisor 7,0, NCSS and PASS 2011, EAST, EAST SURV, EAST Adapt
  • Adaptive Designs: ExpDesign Studio, ADDPLAN
  • Shareware: R, SaTScan for spatial analyses, WinBugs, MD Anderson Biostatistics Software
  • Bioinformatics: Bioconductor R package, GSE A-P for gene set analyses, JMP Genomics
  • RNA-seq data: Deseq and EdgeR packages
  • Pathway analyses: Ingenuity, KEGG
  • Oncomine

BB SRF Project Log and Tracking System

MCC Custom Database Applications

The Cancer Research Informatics SRF, in collaboration with BB SRF personnel, works closely with MCC investigators to develop database applications needed for a specific project.