R Observatory: Metrics for driveR version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

driveR

0.5.0Package record

Prioritizing Cancer Driver Genes Using Genomics Data

0packages depend

3.5Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ege UlgenCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.5.0

Major Changes

added support for gene-level SCNA data frames to be used as input for create_features_df() and added an example gene-level SCNA data frame example_gene_scna_table

Minor changes and bug fixes

Moved org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene and TxDb.Hsapiens.UCSC.hg38.knownGene from "Imports" to "Suggests" per new CRAN policy. Relevant functions raise error if the required package is not installed.

From NEWS.md in the release

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. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

Health

CRAN checks

13OK

CRAN check page ↗

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

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-27
ERROR12 OK, 1 ERROR2026-06-21
OK13 OK2026-06-09

Show 8 earlier changesHide 8 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10
ERROR12 OK, 1 ERROR2026-05-03
OK13 OK2026-05-02
ERROR11 OK, 1 ERROR2026-04-25
NOTE11 OK, 3 NOTE2026-04-16
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 295 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.5.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 17includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

How to use driveR HTML

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #9,053 · ~10/day · ~290/mo

Releases R versions

Daily download trend is not available in this view yet.

40430 days

1.1K90 days

3.5K1 year

Compare downloads with other packages →

Also on1.6K r2u

How downloads are counted

Repository

egeulgen/driver ↗Account: egeulgen

17Stars

1Forks

0Open issues

0Open PRs

7Releases

215Commits

1Commit identities

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

215 commits · Last activity 2025-12-22 · Default branch at 0.5.0.9000, ahead of CRAN 0.5.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-07 · 172026-07-07 · 17

How these are measured

PracticesBeta

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

Checks run against github.com/egeulgen/driver on 2026-10-22.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-12-22 · The repository has a site deploy workflow

pkgdown site last built 2025-12-22

Coverage (1)

Coverage reporting (Codecov)

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing driveR adds 64 packages (35 with compiled code, 48 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB. 4 more not on CRAN are not measured.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Ege Ulgen

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
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
record
2023-08-19 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.4.0
record
2022-08-15 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
record
2022-01-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.2.1
record
2020-11-26 · diff ↗
0.2.0
record
2020-11-19 · diff ↗
0.1.1
record
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

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' entry:

citation("driveR")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1186/s12859-021-04203-7.

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 driveR version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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