R Observatory: Metrics for Rediscover version 0.3.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Rediscover

0.3.3

Identify Mutually Exclusive Mutations

0packages depend

4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Juan A. Ferrer-BonsomsFirst published 2021-04-076 releasesCRAN page ↗

An optimized method for identifying mutually exclusive genomic events. Its main contribution is a statistical analysis based on the Poisson-Binomial distribution that takes into account that some samples are more mutated than others. See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels. (2016) "A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence." Genome biology 17.1 : 1-17. doi:10.1186/s13059-016-1114-x]. The mutations matrices are sparse matrices. The method developed takes advantage of the advantages of this type of matrix to save time and computing resources.

Install

R (CRAN)Ubuntu (r2u)

install.packages("Rediscover", 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-rediscover

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: 4.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.54

not tracked

Coverage

100%

Documentation · exports

10

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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 285 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 100%
Return-value docs: 80%
References docs: 7%

Downloads

4K

CRAN downloads in the past year

Rank #9,745 · ~11/day · ~336/mo

Releases R versions

Daily download trend is not available in this view yet.

37330 days

99390 days

4K1 year

Compare downloads with other packages →

Also on191 r2u

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (6)

R >= 4.0MatrixPoissonBinomial ShiftConvolvePoibinutilsmatrixStats

Imports (5)

maftools data.tableparallelRColorBrewermethods

LinkingTo (0)

none

Suggests (9)

knitr rmarkdown RUnit BiocStyle dplyr kableExtra magick qvalue testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Juan A. Ferrer-Bonsoms

Author, Maintainer · added in 0.3.1

Authors (3)

Juan A. Ferrer-Bonsoms

Author, Maintainer · added in 0.3.1

Laura Jareno

Author · added in 0.3.1

Angel Rubio

Author · added in 0.3.3

Listed in earlier versions (4)

Juan A. Ferrer-Bonsoms Developer

no longer listed · 0.1.0 to 0.3.0

Laura Jareno Developer

no longer listed · 0.1.0 to 0.3.0

Angel Rubio User

no longer listed · 0.1.0 to 0.3.0

and Angel Rubio

no longer listed · 0.3.1 to 0.3.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.3Latest
2025-12-19 · current release · diff ↗
unarchivedReturned to CRAN
2025-12-19
archivedRemoved from CRAN
2025-12-17
issues were not corrected in time
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.3.2
2023-04-14 · diff ↗
unarchivedReturned to CRAN
2023-04-14
archivedRemoved from CRAN
2023-03-31
requires archived package 'speedglm'
0.3.1
2023-02-12 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.0
2021-10-06 · diff ↗
0.2.0
2021-07-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.0
2021-04-07

Show 1 earlier events

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-04-07
Total releases: 6 / 5 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.0
Bundled data: 819 KB / 8 files
Download size: 3.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Rediscover")

Format

Ferrer-Bonsoms, J. A., Jareno, L., & Rubio, A. (2025). Rediscover: Identify Mutually Exclusive Mutations (Version 0.3.3) [Computer software]. https://doi.org/10.32614/CRAN.package.Rediscover

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 Rediscover version 0.3.3 [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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