driveR

0.5.0

Prioritizing Cancer Driver Genes Using Genomics Data

0packages depend

2.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ege UlgenFirst published 2020-11-187 releasesCRAN page ↗GitHub ↗

Cancer genomes contain large numbers of somatic alterations but few genes drive tumor development. Identifying cancer driver genes is critical for precision oncology. Most of current approaches either identify driver genes based on mutational recurrence or using estimated scores predicting the functional consequences of mutations. 'driveR' is a tool for personalized or batch analysis of genomic data for driver gene prioritization by combining genomic information and prior biological knowledge. As features, 'driveR' uses coding impact metaprediction scores, non-coding impact scores, somatic copy number alteration scores, hotspot gene/double-hit gene condition, 'phenolyzer' gene scores and memberships to cancer-related KEGG pathways. It uses these features to estimate cancer-type-specific probability for each gene of being a cancer driver using the related task of a multi-task learning classification model. The method is described in detail in Ulgen E, Sezerman OU. 2021. driveR: driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. BMC Bioinformatics doi:10.1186/s12859-021-04203-7.

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("driveR", 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("egeulgen/driveR")

Development version from egeulgen/driveR. 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-driver

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

Health

CRAN checks

13OK

Slowest check: 3.9 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.24

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-27
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-21
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-10
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 6 earlier snapshots

ERROR2026-05-03
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-25
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-16
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 295 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

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

Downloads

2.9K

CRAN downloads in the past year

Rank #12,973 · ~8/day · ~243/mo

Releases R versions

Daily download trend is not available in this view yet.

28130 days

79690 days

2.9K1 year

Compare downloads with other packages →

Also on1.6K r2u

Repository

GitHub ↗ egeulgen/driver

17Stars

1Forks

0Open issues

0Open PRs

7Releases

215Commits

1Contributors

cancer-drivernessidentify-driver-genesscoringranking-genesdriver-gene-prioritizationdriver

215 commits · Last activity 2025-12-22

Stars over time

2025-05-07 · 172026-07-07 · 17

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/egeulgen/driver on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (7)

caret randomForest GenomicRanges GenomeInfoDb GenomicFeatures S4Vectors rlang

LinkingTo (0)

none

Suggests (7)

org.Hs.eg.db TxDb.Hsapiens.UCSC.hg19.knownGene TxDb.Hsapiens.UCSC.hg38.knownGene testthat covr knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Ege Ulgen

Author, Maintainer, Copyright holder

Authors (1)

Ege Ulgen

Author, Maintainer, Copyright holder

Ege Ulgen

Author, Maintainer, Copyright holder

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
2025-12-22 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.1
2023-08-19 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.0
2022-08-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
2022-01-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.1
2020-11-26 · diff ↗
0.2.0
2020-11-19 · diff ↗
0.1.1
2020-11-18
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-11-18
Total releases: 7 / 6 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0
Bundled data: 1.5 MB / 8 files
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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