Package: diffdriver
Type: Package
Title: Identify Differential Selection
Version: 0.1.7
Authors@R: c(
    person("Siming", "Zhao", , "siming.zhao@dartmouth.edu", role = c("aut", "cre")),
    person("Jie", "Zhou", role = "aut"),
    person("Qirui", "Zhang", role = "aut")
  )
Maintainer: Siming Zhao <siming.zhao@dartmouth.edu>
Description: 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>.
URL: https://szhaolab.github.io/diffdriver/,
        https://github.com/szhaolab/diffdriver
License: MIT + file LICENSE
Encoding: UTF-8
Imports: Matrix, stats, data.table, brglm, fastTopics, SQUAREM
Suggests: knitr, rmarkdown, logging, testthat (>= 3.0.0)
RoxygenNote: 7.2.3
Config/testthat/edition: 3
Depends: R (>= 3.5.0)
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-06-22 16:12:45 UTC; ld-zhangqr
Author: Siming Zhao [aut, cre],
  Jie Zhou [aut],
  Qirui Zhang [aut]
Repository: CRAN
Date/Publication: 2026-06-26 09:50:10 UTC
