{ "cells": [ { "attachments": {}, "cell_type": "markdown", "id": "85543ecd-189d-4cf8-a630-6b76d35fcac3", "metadata": { "id": "dHIW58We8xLx" }, "source": [ "# Pathway analysis with AUCell\n", "\n", "Single-cell RNA sequencing (scRNA-seq) is a powerful tool for exploring variations in cell types between conditions, tissue types, species, and individuals. When conducting scRNA-seq analysis, the differential gene expression (DEG) analysis of the single-cell data is almost always followed by gene set enrichment analysis. The aim of this analysis is to identify gene programs and biological processes, gene ontologies, or regulatory pathways that are overrepresented in a case group compared to a control group.\n", "\n", "Paper: [AUCell: Identifying cells with active gene sets](https://bioconductor.org/packages/AUCell)\n", "\n", "Code: https://github.com/aertslab/AUCell\n", "\n", "Colab_Reproducibility๏ผhttps://colab.research.google.com/drive/1Rk7Zopil-Ve1WFRQLV_AZOwCHRyhsOXk?usp=sharing\n", "\n", "
Warning
\n", "\n", " There are many methods to determine the enrichment pathway between two groups, and the choice of method can significantly impact the conclusion.\n", "
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