R Observatory: Metrics for diffdriver version 0.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

diffdriver

0.1.7

Identify Differential Selection

0packages depend

433downloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Siming ZhaoFirst published 2026-06-261 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("diffdriver", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("szhaolab/diffdriver")

Development version from szhaolab/diffdriver. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-diffdriver

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-diffdriver

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-diffdriver

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-27
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 54 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 90%
Return-value docs: 100%
References docs: 0%

Downloads

433

CRAN downloads in the past year

Rank #23,291 · ~1/day · ~36/mo

Releases R versions

Daily download trend is not available in this view yet.

17630 days

43390 days

4331 year

Compare downloads with other packages →

Also on13 r2u1 autocran

Repository

GitHub ↗ szhaolab/diffdriver

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-07-11

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/szhaolab/diffdriver on 2026-08-09.

Reproducibility and dev environment (1)

data-raw/

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (6)

Matrixstatsdata.table brglm fastTopics SQUAREM

LinkingTo (0)

none

Suggests (4)

knitr rmarkdown logging testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Siming Zhao

Author, Maintainer

Authors (3)

Siming Zhao

Author, Maintainer

Qirui Zhang

Author

Jie Zhou

Author

Package Timeline

1 release. R releases are shown for context.

0.1.7Latest
2026-06-26 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-26
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("diffdriver")

Format

Zhao, S., Zhang, Q., & Zhou, J. (2026). diffdriver: Identify Differential Selection (Version 0.1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.diffdriver

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for diffdriver version 0.1.7 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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