ICBioMark: Data-Driven Design of Targeted Gene Panels for EstimatingImmunotherapy Biomarkers
Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) <doi:10.48550/arXiv.2102.04296>. This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.
| Version: | 0.1.4 |
| Depends: | R (≥ 2.10) |
| Imports: | stats, utils,glmnet,Matrix,dplyr,purrr,latex2exp,matrixStats,ggplot2,gglasso,PRROC |
| Suggests: | testthat (≥ 2.1.0) |
| Published: | 2021-11-15 |
| DOI: | 10.32614/CRAN.package.ICBioMark |
| Author: | Jacob R. Bradley [aut, cre], Timothy I. Cannings [aut] |
| Maintainer: | Jacob R. Bradley <cobrbradley at gmail.com> |
| License: | MIT + fileLICENSE |
| NeedsCompilation: | no |
| Materials: | README,NEWS |
| In views: | Omics |
| CRAN checks: | ICBioMark results |
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