R Observatory: Metrics for omicwas version 0.8.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

omicwas

0.8.0Package record

Cell-Type-Specific Association Testing in Bulk Omics Experiments

0packages depend

3.2Kdownloads / year

71.1%test coverage

11/13flavors OK

Overview

About

Maintained by Fumihiko TakeuchiCRAN page ↗GitHub ↗Issues ↗

In bulk epigenome/transcriptome experiments, molecular expression is measured in a tissue, which is a mixture of multiple types of cells. This package tests association of a disease/phenotype with a molecular marker for each cell type. The proportion of cell types in each sample needs to be given as input. The package is applicable to epigenome-wide association study (EWAS) and differential gene expression analysis. Takeuchi and Kato (submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome association study".

Install

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

install.packages("omicwas", 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("fumi-github/omicwas")

Development version from fumi-github/omicwas. 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-omicwas

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-omicwas

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-omicwas

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Fumihiko Takeuchi <fumihiko@takeuchi.name>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘ctassoc.Rd’:
    https://doi.org/10.1080/03610927608827353

CRAN check page ↗

Slowest check: 3.4 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-06-09
ERROR11 OK, 1 NOTE, 1 ERROR2026-06-08
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.8.0

READMEYes · 80 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 6
Examples that run: 67%4 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 90%
Return-value docs: 100%
Help pages citing references: 33%

Vignettes (1)

Introduction to omicwas HTML

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #14,087 · ~9/day · ~265/mo

Releases R versions

Daily download trend is not available in this view yet.

34430 days

83690 days

3.2K1 year

Compare downloads with other packages →

Also on119 r2u7 autocran68 c2d4u

How downloads are counted

Repository

fumi-github/omicwas ↗Account: fumi-github

6Stars

2Forks

0Open issues

0Open PRs

7Releases

218Commits

1Commit identities

218 commits · Last activity 2021-03-23 · 0% stars, 30d

Responsiveness

not measured

Stars over time

2025-03-19 · 52026-08-14 · 6

How these are measured

PracticesBeta

Checks run against github.com/fumi-github/omicwas on 2026-10-21.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing omicwas adds 32 packages (20 with compiled code, 32 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, glmnet 2.7 MB.

Depends (1)

R >= 3.6.0

Imports (12)

broom data.table dplyr ff glmnet magrittrMASSmatrixStatsparallelpurrr rlang tidyr

LinkingTo (0)

none

Suggests (3)

testthat knitr rmarkdown

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 (1)

Fumihiko Takeuchi

Author, Maintainer since 0.3.1 (2020)

Releases (3)

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.8.0Latest
record
2020-10-08 · current release · diff ↗ ·
removed 1 export
ctRUV
0.7.0
record
2020-06-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3.1
record
2020-02-19
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-02-19
Total releases: 3 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.6.0
Bundled data: 3.2 MB / 3 files
Download size: 3.8 MB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("omicwas")

Format

Takeuchi, F. (2020). omicwas: Cell-Type-Specific Association Testing in Bulk Omics Experiments (Version 0.8.0) [Computer software]. https://doi.org/10.32614/CRAN.package.omicwas

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 omicwas version 0.8.0 [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.

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