---
name: Differential Gene Expression
version: 0.1.0
author: Christophe Avenel
date: 2023-08-08
image: DGE.gif
description:
  Use the DGE plugin to display Differential Gene Expression computed with Scanpy (https://scanpy.readthedocs.io/en/stable/generated/scanpy.tl.rank_genes_groups.html).<br/>
  Your data must be in the AnnData format, and the selected observation should be pre-processed using the rank_genes_groups function in Scanpy:<br/>
  <pre>
  import scanpy as sc<br/>
  adata = sc.read('path/to/your/data.h5ad')<br/>
  sc.tl.rank_genes_groups(adata, groupby='cluster_name', method='wilcoxon', key_added='cluster_name_wilcoxon')
  </pre>
  Note that it is important that the key_added parameter is set to the same name as the observation, plus "_wilcoxon".<br/>
  In the future, more methods will be available.<br/>
  <br/>
  You can then click on any cluster to display the top 25 genes that are differentially expressed in this cluster, as well as the lowest 25 genes.<br/>
  By selecting the genes in the chart, you can display the sum of the expression of these genes on the data.<br/>