R Observatory: Metrics for DEET version 1.0.12

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DEET

1.0.12Package record

Differential Expression Enrichment Tool

0packages depend

6.6Kdownloads / year

32.2%test coverage

13/13flavors OK

Overview

About

Maintained by Dustin SokolowskiCRAN page ↗

Abstract of Manuscript. Differential gene expression analysis using RNA sequencing (RNA-seq) data is a standard approach for making biological discoveries. Ongoing large-scale efforts to process and normalize publicly available gene expression data enable rapid and systematic reanalysis. While several powerful tools systematically process RNA-seq data, enabling their reanalysis, few resources systematically recompute differentially expressed genes (DEGs) generated from individual studies. We developed a robust differential expression analysis pipeline to recompute 3162 human DEG lists from The Cancer Genome Atlas, Genotype-Tissue Expression Consortium, and 142 studies within the Sequence Read Archive. After measuring the accuracy of the recomputed DEG lists, we built the Differential Expression Enrichment Tool (DEET), which enables users to interact with the recomputed DEG lists. DEET, available through CRAN and RShiny, systematically queries which of the recomputed DEG lists share similar genes, pathways, and TF targets to their own gene lists. DEET identifies relevant studies based on shared results with the user’s gene lists, aiding in hypothesis generation and data-driven literature review. Sokolowski, Dustin J., et al. "Differential Expression Enrichment Tool (DEET): an interactive atlas of human differential gene expression." Nucleic Acids Research Genomics and Bioinformatics (2023).

Install

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

install.packages("DEET", 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-deet

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-DEET

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-DEET

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: 2.8 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 1.0.12

READMEYes · 878 wordsVignettesYes · 1 · staticNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 13
Examples that run: 85%11 run in a plain check · 2 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: 38%

Vignettes (1)

Differential Expression Enrichment Tool (DEET)

How these are measured

Downloads

6.6K

CRAN downloads in the past year

Rank #7,299 · ~18/day · ~550/mo

Releases R versions

Daily download trend is not available in this view yet.

45030 days

1.2K90 days

6.6K1 year

Compare downloads with other packages →

Also on75 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing DEET adds 37 packages (18 with compiled code, 32 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, ActivePathways 3.0 MB.

Depends (1)

R >= 3.5.0

Imports (9)

ActivePathways pbapply dplyr ggplot2 glmnetutilsstatsggrepel downloader

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 (7)

Dustin Sokolowski

Author, Maintainer since 1.0.2 (2022)

Jedid Ahn

Author

Kai Ellis

Author · added in 1.0.5

Author

Author

Author

Author

Releases (8)

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
1.0.12Latest
record
2024-06-26 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.11
record
2023-08-17 · diff ↗
1.0.10
record
2023-05-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2023-01-05
1.0.8
record
2023-01-05 · diff ↗
archivedRemoved from CRAN
2022-12-21
email to the maintainer was undeliverable
1.0.7
record
2022-12-15 · diff ↗ ·
added 3 exports
DEET_Input_as_Reference, DEET_enrich_genesonly, adjust_DE_cutoffs
1.0.6
record
2022-10-10 · diff ↗
1.0.5
record
2022-07-19 · diff ↗
1.0.2
record
2022-06-27
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-06-27
Total releases: 8 / 4 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.7 MB / 4 files
Download size: 1.8 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DEET")

Format

Sokolowski, D., Ahn, J., Ellis, K., Erdman, L., Goldenberg, A., Hou, H., & Wilson, M. (2024). DEET: Differential Expression Enrichment Tool (Version 1.0.12) [Computer software]. https://doi.org/10.32614/CRAN.package.DEET

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 DEET version 1.0.12 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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