BSRF 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 at http://sweb.uky.edu/~emva222/RPackage.html.
- BEAU is an R package developed by 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 at: http://sweb.uky.edu/~cwa236/BEAU/
- Stacey Slone and Emily Van Meter have been developing email notifications for interim analyses and safety triggers that integrate with the OnCore system to assist with implementation of investigator-initiated clinical trials at MCC. Please email Stacey for more information at firstname.lastname@example.org.
- 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 email@example.com.
BSRF 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
BSRF Project Log and Tracking System
MCC Custom Database Applications
The Cancer Research Informatics SRF, in collaboration with BSRF personnel, works closely with MCC investigators to develop database applications needed for a specific project.