DEET

1.0.12

Differential Expression Enrichment Tool

0packages depend

7.2Kdownloads / year

32.2%test coverage

13/13checks pass

Overview

About

Maintained by Dustin SokolowskiFirst published 2022-06-278 releasesCRAN 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)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.

bspm (used by r2u) also needs make: sudo apt install make

# 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).

Health

CRAN checks

13OK

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.03

32.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 878 wordsVignettesYes · staticpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 100%
Return-value docs: 100%
References docs: 38%

Downloads

7.2K

CRAN downloads in the past year

Rank #5,707 · ~20/day · ~596/mo

Releases R versions

Daily download trend is not available in this view yet.

39530 days

1.6K90 days

7.2K1 year

Compare downloads with other packages →

Also on97 r2u42 autocran

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

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.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Dustin Sokolowski

Author, Maintainer

Authors (7)

Dustin Sokolowski

Author, Maintainer

Jedid Ahn

Author

Kai Ellis

Author · added in 1.0.5

Author

Author

Author

Author

Package Timeline

8 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
1.0.12Latest
2024-06-26 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.0.11
2023-08-17 · diff ↗
1.0.10
2023-05-01 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.0.8
2023-01-05 · diff ↗
unarchivedReturned to CRAN
2023-01-05
archivedRemoved from CRAN
2022-12-21
email to the maintainer was undeliverable
1.0.7
2022-12-15 · diff ↗
1.0.6
2022-10-10 · diff ↗
1.0.5
2022-07-19 · diff ↗
1.0.2
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
Installed size: not tracked yet
With dependencies: not tracked yet

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