diffdriver: Identify Differential Selection
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 |
Documentation:
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