R Observatory: Metrics for ActiveDriverWGS version 1.2.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ActiveDriverWGS

1.2.1Package record

A Driver Discovery Tool for Cancer Whole Genomes

0packages depend

4.4Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Juri ReimandCRAN page ↗

A method for finding enrichments of somatic single nucleotide variants (SNVs) and small insertions-deletions (Indels) in functional elements in the human genome. 'ActiveDriverWGS' detects coding and noncoding cancer driver elements using whole genome sequencing data. The method is part of the publication H. Zhu et al. (2020) doi:10.1016/j.molcel.2019.12.027 "Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks" in Molecular Cell.

Changes in 1.2.1

Bug fixed: elements and sites with coordinates below 2 or beyond the chromosome end now return an informative error, preventing downstream failures in trinucleotide context calculations.
Bug fixed: all GenomicRanges operations (findOverlaps, setdiff, intersect, union) now use ignore.strand = TRUE, ensuring mutations, elements, and sites are always matched by genomic position regardless of strand.

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)

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

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

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-activedriverwgs

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: 4.0 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-10

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-05-03
OK12 OK2026-04-25
NOTE4 OK, 1 NOTE2026-03-14

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.1

READMEYes · 396 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.2.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 63%5 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 21%

Vignettes (1)

ActiveDriverWGS

How these are measured

Downloads

4.4K

CRAN downloads in the past year

Rank #5,604 · ~12/day · ~370/mo

Releases R versions

Daily download trend is not available in this view yet.

48030 days

1.5K90 days

4.4K1 year

Compare downloads with other packages →

Also on92 r2u

How downloads are counted

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing ActiveDriverWGS adds 0 packages. 6 more not on CRAN are not measured.

Depends (1)

R >= 3.5

Imports (6)

BSgenome Biostrings GenomeInfoDb GenomicRanges IRanges S4Vectors

LinkingTo (0)

none

Suggests (7)

BSgenome.Hsapiens.UCSC.hg19 BSgenome.Hsapiens.UCSC.hg38 BSgenome.Mmusculus.UCSC.mm9 BSgenome.Mmusculus.UCSC.mm10 knitr testthat 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 (3)

Juri Reimand

Author, Maintainer since 1.1.0 (2020)

Kevin Cheng

Contributor · added in 1.2.0

Helen Zhu

Contributor

Previously maintained by Helen Zhu (1.0.1).

Releases (6)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-03-13
1.2.1Latest
record
2026-03-13 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-11-16
issues were not corrected in time Requires BioC data packages
R
R 4.3.0 released · 2023-04-21
1.2.0
record
2022-09-03 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.1.2
record
2021-11-30 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.1.1
record
2020-09-17 · diff ↗
1.1.0
record
2020-09-07 · diff ↗ ·
added 1 export
prepare_elements_from_BED4
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
1.0.1
record
2019-03-22

Show 1 earlier eventHide 1 earlier event

R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-22
Total releases: 6 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5
Bundled data: 394 KB / 3 files
Download size: 618 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ActiveDriverWGS")

Format

Reimand, J., Cheng, K., & Zhu, H. (2026). ActiveDriverWGS: A Driver Discovery Tool for Cancer Whole Genomes (Version 1.2.1) [Computer software]. https://doi.org/10.32614/CRAN.package.ActiveDriverWGS

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 ActiveDriverWGS version 1.2.1 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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