R Observatory: Metrics for OmicsQC version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

OmicsQC

1.1.1

Nominating Quality Control Outliers in Genomic Profiling Studies

0packages depend

2.3Kdownloads / year

92.0%test coverage

13/13checks pass

Overview

About

Maintained by Paul C. BoutrosFirst published 2024-03-012 releasesCRAN page ↗

A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.

Install

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

install.packages("OmicsQC", 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-omicsqc

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-OmicsQC

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-OmicsQC

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

Health

CRAN checks

13OK

Slowest check: 1.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.72

92.0%

Coverage · measured lines

100%

Documentation · exports

5

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
OK2026-03-12
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

2.3K

CRAN downloads in the past year

Rank #18,037 · ~6/day · ~192/mo

Releases R versions

Daily download trend is not available in this view yet.

15930 days

62090 days

2.3K1 year

Compare downloads with other packages →

Also on137 r2u23 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (5)

statsutilsfitdistrplus lsa BoutrosLab.plotting.general

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown kableExtra dplyr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Paul C. Boutros

Author, Maintainer

Authors (3)

Paul C. Boutros

Author, Maintainer

Anders Hugo Frelin

Author

Helen Zhu

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
2026-01-24 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0
2024-03-01
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-03-01
Total releases: 2 / 2 yrs
License: GPL-2 OSI
Minimum R: ≥ 2.10
Bundled data: 15 KB / 3 files
Download size: 1.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Anomaly Detection

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("OmicsQC")

Format

Boutros, P. C., Frelin, A. H., & Zhu, H. (2026). OmicsQC: Nominating Quality Control Outliers in Genomic Profiling Studies (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.OmicsQC

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 OmicsQC version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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