R Observatory: Metrics for tmod version 0.50.13

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tmod

0.50.13

Feature Set Enrichment Analysis for Metabolomics and Transcriptomics

0packages depend

7.5Kdownloads / year

28.4%test coverage

0/13checks pass

Overview

About

Maintained by January WeinerFirst published 2015-06-1912 releasesCRAN page ↗GitHub ↗

Methods and feature set definitions for feature or gene set enrichment analysis in transcriptional and metabolic profiling data. Package includes tests for enrichment based on ranked lists of features, functions for visualisation and multivariate functional analysis. See Zyla et al (2019) doi:10.1093/bioinformatics/btz447.

Install

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

install.packages("tmod", 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("january3/tmod")

Development version from january3/tmod. 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-tmod

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-tmod

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-tmod

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 3.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 2.42

28.4%

Coverage · measured lines

100%

Documentation · exports

15

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 159 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 77%
Documented parameters: 95%
Return-value docs: 71%
References docs: 5%

Downloads

7.5K

CRAN downloads in the past year

Rank #8,562 · ~21/day · ~628/mo

Releases R versions

Daily download trend is not available in this view yet.

28430 days

1.1K90 days

7.5K1 year

Compare downloads with other packages →

Also on148 r2u17 autocran1.5K conda_forge24 c2d4u

Repository

GitHub ↗ january3/tmod

4Stars

3Forks

2Open issues

0Open PRs

1Releases

132Commits

2Contributors

132 commits · Last activity 2025-12-01 · 0% stars, 30d

Stars over time

2023-12-22 · 32026-07-07 · 4

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/january3/tmod on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (15)

beeswarm tagcloud XMLmethodsplotwidgets RColorBrewer gplots tibble pheatmap ggplot2 tidyr purrr rlang tidyselect ggrepel

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown dplyr pander cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

January Weiner

Author, Maintainer

Authors (1)

January Weiner

Author, Maintainer

Package Timeline

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

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
0.50.13Latest
2023-03-31 · current release · diff ↗
0.50.11
2022-09-26 · diff ↗
unarchivedReturned to CRAN
2022-09-26
archivedRemoved from CRAN
2022-09-22
requires archived package 'colorDF'
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.46.2
2020-10-02 · diff ↗
0.44
2020-06-18 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.40
2018-11-29 · diff ↗
R
R 3.5.0 released · 2018-04-23

Show 13 earlier events

0.36
2018-03-10 · diff ↗
unarchivedReturned to CRAN
2018-03-10
archivedRemoved from CRAN
2018-02-20
check problems were not corrected despite reminders Unconditional use of Suggests package(s) from BioC Did not declare 'rmarkdown' for vignette engine
R
R 3.4.0 released · 2017-04-21
0.31
2016-09-08 · diff ↗
0.30
2016-08-05 · diff ↗
0.27
2016-06-04 · diff ↗
0.26
2016-05-18 · diff ↗
R
R 3.3.0 released · 2016-05-03
archivedRemoved from CRAN
2016-05-02
check problems were not corrected despite reminders
0.24
2016-02-26 · diff ↗
0.19
2015-06-19
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-06-19
Total releases: 12 / 11 yrs
License: GPL (>= 2.0)
Minimum R: ≥ 2.10
Bundled data: 1.8 MB / 8 files
Download size: 2.9 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tmod")

Format

Weiner, J. (2023). tmod: Feature Set Enrichment Analysis for Metabolomics and Transcriptomics (Version 0.50.13) [Computer software]. https://doi.org/10.32614/CRAN.package.tmod

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 tmod version 0.50.13 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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