DEET_feature_extract_example_matrix

<p>An object of class data.frame where rows are genes and columns are comparisons.
The matrix is populated by the log2Fold-change of each gene within each study.
If the gene is not detected within that study, it is populated with 0 instead of the log2Fold-change.
This object is inputted into the `mat` input variable for the `DEET_feature_extract` function.
This example takes 1000 random genes and 200 random studies (seed = 1234s).</p>

datasets

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).

Dustin Sokolowski

DEET

Differential Expression Enrichment Tool

Jedid Ahn

Lauren Erdman

Kai Ellis

Huayun Hou

Anna Goldenberg

Michael Wilson

DEET_feature_extract_example_matrix function

<p>An object of class data.frame where rows are genes and columns are comparisons (1000 randomly selected genes and 200 randomly selected studies).</p>

Format

DEET_feature_extract_example_matrix — DEET_feature_extract_example_matrix

DEET_feature_extract_example_matrix: DEET_feature_extract_example_matrix

Description

Usage

Arguments

Format

Examples