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    • Online Integration
    • customDEG
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  • Input
  • Output
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  1. Tool

customDEG

PreviousOnline Integration

Last updated 6 months ago

While we provide pre-calculated DEGs on the DEG page, these are generated within the same atlas, comparing one cell type against all others. However, some users may require more tailored analyses. To meet this need, we offer CustomDEG, which allows users to compare cells from any two selected groups, either within the same atlas or across different atlases, enabling more flexible and in-depth exploration of differential gene expression.

Input

Users only need to select two groups of cells for CustomDEG. The cells in group 2 will serve as the baseline in the analysis (group 1 versus group 2)

Each option in the selection represents a cell type from a specific atlas. For each group, users can select one or multiple cell types.

Output

The output table contains the top 100 DEGs, sorted by adjusted p-value and log fold change. The table includes five columns:

  • Gene: The gene symbol of the DEG.

  • LogFC: The log fold change. A positive value indicates higher gene expression in group 1. For example, this would mean higher expression in blood memory B cells compared to bone marrow memory B cells.

  • Adjusted p: The multiplicity-adjusted p-values of the DEGs.

  • Pct1: The percentage of cells in group 1 expressing the gene.

  • Pct2: The percentage of cells in group 2 expressing the gene.

Analysis

The DEGs are calculated using the R package Presto (https://github.com/immunogenomics/presto), which applies the Wilcoxon rank sum test.