DEET: Differential Expression Enrichment Tool

RNA sequencing (RNA-seq) followed by differential gene expression analyses is a fundamental approach for making biological discoveries. Ongoing large-scale efforts to systematically process and normalize publicly available gene expression data facilitate rapid reanalyses of specific studies and the development of new methods for querying it. While there are several powerful tools for querying systematically processed publicly available RNA-seq data at the individual sample level, there are fewer options for querying differentially expressed gene (DEG) lists generated from these experiments. Here, we present the Differential Expression Enrichment Tool (DEET), which allows users to interact with 3162 consistently processed DEG lists curated from 142 RNA-seq datasets obtained from recount2 database, which contains data from consortiums (GTex, TCGA) and individual labs (SRA). To establish DEET we integrated systematically processed human RNA-seq data from recount2 with reported and predicted metadata from multiple sources and developed a CRAN R package and Shiny App where users can compare their genes, p-values, and coefficients against the DEG lists within DEET. Here we present DEET and demonstrate how it can facilitate hypothesis generation and provide biological insight from user-defined differential gene expression results. Reference: Sokolowski,D.J., Ahn J., Erdman,L., Hou,H., Ellis,K., Wang L., Goldenberg,A., and Wilson,M.D. (2022) Differential Expression Enrichment Tool (DEET): An interactive atlas of human differential gene expression. (In Preparation).

Version: 1.0.6
Depends: R (≥ 3.5.0)
Imports: ActivePathways, pbapply, dplyr, ggplot2, glmnet, utils, stats, ggrepel, downloader
Suggests: testthat, knitr, rmarkdown
Published: 2022-10-10
Author: Dustin Sokolowski [aut, cre], Jedid Ahn [aut], Lauren Erdman [aut], Kai Ellis [aut], Huayun Hou [aut], Anna Goldenberg [aut], Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski at sickkids.ca>
License: GPL-3
NeedsCompilation: no
Materials: README
CRAN checks: DEET results

Documentation:

Reference manual: DEET.pdf
Vignettes: Differential Expression Enrichment Tool (DEET)

Downloads:

Package source: DEET_1.0.6.tar.gz
Windows binaries: r-devel: DEET_1.0.6.zip, r-release: DEET_1.0.6.zip, r-oldrel: DEET_1.0.6.zip
macOS binaries: r-release (arm64): DEET_1.0.6.tgz, r-oldrel (arm64): DEET_1.0.6.tgz, r-release (x86_64): DEET_1.0.6.tgz, r-oldrel (x86_64): DEET_1.0.6.tgz
Old sources: DEET archive

Linking:

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