R Observatory: Metrics for combiroc version 0.3.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

combiroc

0.3.4Package record

Selection and Ranking of Omics Biomarkers Combinations Made Easy

0packages depend

3.5Kdownloads / year

69.3%test coverage

13/13flavors OK

Overview

About

Maintained by Riccardo L. RossiCRAN page ↗GitHub ↗Issues ↗

Provides functions and a workflow to easily and powerfully calculating specificity, sensitivity and ROC curves of biomarkers combinations. Allows to rank and select multi-markers signatures as well as to find the best performing sub-signatures, now also from single-cell RNA-seq datasets. The method used was first published as a Shiny app and described in Mazzara et al. (2017) doi:10.1038/srep45477 and further described in Bombaci & Rossi (2019) doi:10.1007/978-1-4939-9164-8_16, and widely expanded as a package as presented in the bioRxiv pre print Ferrari et al. doi:10.1101/2022.01.17.476603.

Changes in 0.3.4

This version is aimed at CRAN submission: small edits and variations were made to make it pass the R-CMD-check --as-cran testing, and presubmission CRAN checks have been solved.

Please note that (differently from previous CRAN release) the min_SE and min_SP arguments of markers_distribution() function have now a default value = 0. This means that no threshold values are imposed to SE or SP to be included in the data.frame that contains the coordinates of the above computed ROC.

Thus if the user does not set up any threshold, all SE and SP values are taken into account.

From NEWS.md in the release

Install

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

install.packages("combiroc", 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("ingmbioinfo/combiroc")

Development version from ingmbioinfo/combiroc. 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-combiroc

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-combiroc

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-combiroc

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: 2.3 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.4

READMEYes · 463 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 0.3.4Citation fileNo

Help pages: 13
Examples that run: 0%13 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

3.5K

CRAN downloads in the past year

Rank #10,395 · ~10/day · ~289/mo

Releases R versions

Daily download trend is not available in this view yet.

38730 days

98990 days

3.5K1 year

Compare downloads with other packages →

Also on90 r2u12 autocran

How downloads are counted

Repository

ingmbioinfo/combiroc ↗Organization: ingmbioinfo

6Stars

1Forks

4Open issues

0Open PRs

3Releases

192Commits

5Commit identities

192 commits · Last activity 2026-01-07 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 23
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-10-09 · 52026-08-08 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/ingmbioinfo/combiroc 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 (3)

pkgdown

GitHub Pages site last deployed 2024-06-24 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing combiroc adds 33 packages (18 with compiled code, 31 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, Rcpp 1.8 MB.

Depends (1)

R >= 3.5.0

Imports (9)

tidyr dplyr ggplot2 gtools pROC stringrstatsutilsmoments

LinkingTo (0)

none

Suggests (6)

testthat knitr markdown rmarkdown httr Seurat

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)

Riccardo L. Rossi

Author, Maintainer since 0.2.3 (2021)

Ivan Ferrari

Author

Saveria Mazzara

Author

Mauro Bombaci

ccp, Contributor, Data contributor

Releases (2)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.3.4Latest
record
2023-07-06 · current release · diff ↗ ·
removed 3 exports
classify, load_unclassified_data, se_sp

added 2 exports
combi_score, seurat_to_combiroc
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.2.3
record
2021-08-17
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-17
Total releases: 2 / 5 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 2.6 KB / 2 files
Download size: 2.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("combiroc")

Format

Rossi, R. L., Bombaci, M., Ferrari, I., & Mazzara, S. (2023). combiroc: Selection and Ranking of Omics Biomarkers Combinations Made Easy (Version 0.3.4) [Computer software]. https://doi.org/10.32614/CRAN.package.combiroc

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 combiroc version 0.3.4 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →