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Tests for context-dependent selection on cancer driver genes using somatic mutation data. The package implements the DiffDriver statistical framework to assess whether the strength of positive selection on mutations in a driver gene is associated with tumor- or individual-level context variables, such as clinical traits, genomic features, or immune microenvironment subtypes. DiffDriver estimates individual- and position-specific background mutation rates, models selection as a deviation from the background rate using functional annotations, and tests context effects through a latent-variable logistic model. It provides utilities for preparing mutation and annotation data, fitting differential-selection models, running gene-level association tests, summarizing candidate genes, and visualizing mutation patterns. The method is described in Zhou et al. (2026) "Detecting context-dependent selection on cancer driver genes with DiffDriver" <doi:10.64898/2026.04.06.716771>.
| Version: | 0.1.7 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Matrix, stats, data.table, brglm, fastTopics, SQUAREM |
| Suggests: | knitr, rmarkdown, logging, testthat (≥ 3.0.0) |
| Published: | 2026-06-26 |
| DOI: | 10.32614/CRAN.package.diffdriver (may not be active yet) |
| Author: | Siming Zhao [aut, cre], Jie Zhou [aut], Qirui Zhang [aut] |
| Maintainer: | Siming Zhao <siming.zhao at dartmouth.edu> |
| License: | MIT + file LICENSE |
| URL: | https://szhaolab.github.io/diffdriver/, https://github.com/szhaolab/diffdriver |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | diffdriver results |
| Reference manual: | diffdriver.html , diffdriver.pdf |
| Vignettes: |
A tutorial to run diffdriver (source, R code) |
| Package source: | diffdriver_0.1.7.tar.gz |
| Windows binaries: | r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: | r-release (arm64): not available, r-oldrel (arm64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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