CRAN/E | DEET

DEET

Differential Expression Enrichment Tool

Installation

About

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).

Key Metrics

Version 1.0.11
R ≥ 3.5.0
Published 2023-08-17 247 days ago
Needs compilation? no
License GPL-3
CRAN checks DEET results

Downloads

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Last 30 days 229 -6%
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Maintainer

Maintainer

Dustin Sokolowski

dustin.sokolowski@sickkids.ca

Authors

Dustin Sokolowski

aut / cre

Jedid Ahn

aut

Lauren Erdman

aut

Kai Ellis

aut

Huayun Hou

aut

Anna Goldenberg

aut

Michael Wilson

aut

Material

README
Reference manual
Package source

Vignettes

Differential Expression Enrichment Tool (DEET)

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

DEET archive

Depends

R ≥ 3.5.0

Imports

ActivePathways
pbapply
dplyr
ggplot2
glmnet
utils
stats
ggrepel
downloader

Suggests

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