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DEET
View on CRAN: Click
here
Download and install DEET package within the R console
Install from CRAN:
install.packages("DEET")
Install from Github:
library("remotes")
install_github("cran/DEET")
Install by package version:
library("remotes")
install_version("DEET", "1.0.11")
Attach the package and use:
library("DEET")
Maintained by
Dustin Sokolowski
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-06-27
Latest Update: 2023-08-17
Description:
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
How to cite:
Dustin Sokolowski (2022). DEET: Differential Expression Enrichment Tool. R package version 1.0.11, https://cran.r-project.org/web/packages/DEET
Previous versions and publish date:
Other packages that cited DEET R package
View DEET citation profile
Other R packages that DEET depends,
imports, suggests or enhances
Functions, R codes and Examples using
the DEET R package
Some associated functions: DEET_Input_as_Reference . DEET_data_download . DEET_enrich . DEET_enrich_genesonly . DEET_enrichment_plot . DEET_example_data . DEET_feature_extract . DEET_feature_extract_example_matrix . DEET_feature_extract_example_response . DEET_plot_correlation . adjust_DE_cutoffs . example_DEET_enrich_input . proccess_and_plot_DEET_enrich .
Some associated R codes: DEET_Input_as_Reference.R . DEET_data_download.R . DEET_enrich.R . DEET_enrich_genesonly.R . DEET_enrichment_plot.R . DEET_example_data.R . DEET_feature_extract.R . DEET_feature_extract_example_matrix.R . DEET_feature_extract_example_response.R . DEET_plot_correlation.R . adjust_DE_cutoffs.R . example_DEET_enrich_input.R . proccess_and_plot_DEET_enrich.R . Full DEET package functions and examples
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