R Observatory: Metrics for SelectSim version 0.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SelectSim

0.1.6

Selected Events Linked by Evolutionary Conditions in Cancer

0packages depend

342downloads / year

58.0%test coverage

13/13checks pass

Overview

About

Maintained by Arvind IyerFirst published 2026-07-211 releasesCRAN page ↗GitHub ↗

Implements the 'SelectSim' methodology for identifying patterns of co-occurrence and mutual exclusivity between functional genomic alterations in cancer cohorts. The package processes mutation annotation data, constructs alteration matrices, estimates expected alteration-pair frequencies, and quantifies deviations associated with selective interactions. The methodology is described in Iyer et al. (2026) doi:10.1038/s41588-026-02661-4.

Install

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

install.packages("SelectSim", 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("CSOgroup/SelectSim")

Development version from CSOgroup/SelectSim. 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-selectsim

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-SelectSim

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-SelectSim

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

58.0%

Coverage · measured lines

100%

Documentation · exports

12

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
OK2026-07-29
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-27
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-07-22
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 274 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

342

CRAN downloads in the past year

Rank #24,139 · ~1/day · ~29/mo

Releases R versions

Daily download trend is not available in this view yet.

34230 days

34290 days

3421 year

Compare downloads with other packages →

Also on12 r2u

Repository

GitHub ↗ csogroup/selectsim

4Stars

0Forks

2Open issues

0Open PRs

3Releases

48Commits

1Contributors

cancer-genomicsexome-sequencing-analysismutation-analysis

48 commits · Last activity 2026-07-12 · +33.3% stars, 30d

Stars over time

2026-07-22 · 32026-08-05 · 4

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/csogroup/selectsim on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Governance and community (2)

Issue templatesPR template

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5

Imports (12)

doParallel doRNG dplyr foreach ggplot2 ggpubr ggridgesMatrixparallelRcpp Rfaststats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (4)

knitr rmarkdown testthat tictoc

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Arvind Iyer

Author, Maintainer, Copyright holder

Authors (4)

Arvind Iyer

Author, Maintainer, Copyright holder

Giovanni Ciriello

Author, Copyright holder

Marco Mina

Author

Miljan Petrovic

Author, Copyright holder

Copyright holders (3)

Arvind Iyer

Author, Maintainer, Copyright holder

Giovanni Ciriello

Author, Copyright holder

Miljan Petrovic

Author, Copyright holder

Package Timeline

1 release. R releases are shown for context.

0.1.6Latest
2026-07-21 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-07-21
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5
Bundled data: 2.6 MB / 6 files
Download size: 3.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("SelectSim")

Format

Iyer, A., Ciriello, G., Mina, M., & Petrovic, M. (2026). SelectSim: Selected Events Linked by Evolutionary Conditions in Cancer (Version 0.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.SelectSim

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 SelectSim version 0.1.6 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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