R Observatory: Metrics for SelectSim version 0.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

SelectSim

0.1.6Package record

Selected Events Linked by Evolutionary Conditions in Cancer

0packages depend

946downloads / year

58.0%test coverage

13/13flavors OK

Overview

About

Maintained by Arvind IyerCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.1.6

Removed reshape2 dependency; replaced with base R equivalents (tapply, as.data.frame.table).
Fixed theme_ridges() partial argument match (center → center_axis_labels).
Fixed parallel log file leak in null_model_parallel using tempfile() and on.exit().
Refactored selectX() to eliminate duplicate verbose/non-verbose code paths.
Added utils::globalVariables() declarations to suppress R CMD check NOTEs for ggplot2 aesthetics.
Dropped SystemRequirements: C++14 from DESCRIPTION.
Added GitHub community health files: CONTRIBUTING.md, CODE_OF_CONDUCT.md, issue templates, PR template, and CI workflow.
Expanded test coverage with test-gam_utils.R.
Repository migrated: development moved from personal branches to CSOgroup/SelectSim; dev branch merged into main for initial public release.
Bumped version to 0.1.6 across all source files
Updated citation (inst/CITATION, README) to the published Nature Genetics article: Iyer A, Petrovic M, Sesia D, Nanni L, Mina M, Ciriello G (2026). Evolving patterns of co-mutations from tumor initiation to metastatic progression. *Nature Genetics*. DOI: 10.1038/s41588-026-02661-4

From NEWS.md in the release

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. 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

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

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 6.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-29

Show 2 earlier changesHide 2 earlier changes

ERROR12 OK, 1 ERROR2026-07-27
OK7 OK2026-07-22

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.6

READMEYes · 274 wordsVignettesYes · 2 · dynamicNEWSYes · 67% structured · mentions 0.1.6Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 55
Examples that run: 67%37 run in a plain check · 18 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: 0%

Vignettes (2)

How these are measured

Downloads

946

CRAN downloads in the past year

Rank #17,389 · ~3/day · ~79/mo

Releases R versions

Daily download trend is not available in this view yet.

22530 days

74390 days

9461 year

Compare downloads with other packages →

Also on35 r2u3 autocran

How downloads are counted

Repository

csogroup/selectsim ↗Organization: CSOgroup

4Stars

0Forks

2Open issues

1Open PRs

3Releases

48Commits

1Commit identities

cancer-genomicsexome-sequencing-analysismutation-analysis

48 commits · Last activity 2026-07-12 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 338
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-22 · 32026-08-05 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/csogroup/selectsim on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (4)

Code of conductContributing guideIssue templatesPR template

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-07-12 · The repository has a site deploy workflow

pkgdown site last built 2026-07-12, before release 0.1.6 (2026-07-21)

CRAN release process (1)

cran-comments.md

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing SelectSim adds 78 packages (37 with compiled code, 68 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, doBy 4.3 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Arvind Iyer

Giovanni Ciriello

Author, Copyright holder

Marco Mina

Author

Miljan Petrovic

Author, Copyright holder

Releases (1)

0.1.6Latest
record
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

Cite

Cite this package

Run in R for the authors' entry:

citation("SelectSim")

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

It points to 10.1038/s41588-026-02661-4.

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 v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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