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: 2026-06-26 18:39:42 UTC; root
Author: Siming Zhao [aut, cre], Jie Zhou [aut], Qirui Zhang [aut]
Repository: https://cran.r-universe.dev
Date/Publication: 2026-06-26 09:50:10 UTC
RemoteUrl: https://github.com/cran/diffdriver
RemoteRef: HEAD
RemoteSha: b7416b20d7423843e14f4b4fb5a819b9f0ecd9ae