README.md

Enrichment Analysis

This folder contains notebooks and results for performing cell-type enrichment using the following dataset

• Lab: Kriegstein
• Publication: Velmeshev et al. Science. 2019.
• PubMed Abstract: 31097668
• NCBI Bioproject: PRJNA434002
• Submitted by: Dmitry Velmeshev (2019-10-18), Version 3
• Direct link to this plot for manuscripts: https://autism.cells.ucsc.edu

Contents

• celltype_enrichment_analysis.ipynb: Compute and visualize cell-type enrichment in pseudobulk samples
• differential_expression_edgeR.ipynb: Differential expression analysis with EdgeR on cell-type aggregated counts
• differential_expression_scanpy.ipynb: Differential expression analysis using Scanpy’s ranking methods
• figures/: Directory with key figures generated by these notebooks.

Key Figures

Cell-Type Enrichment Heatmap

Dotplot of enrichment scores for major cell types in pseudobulk samples._

Enrichment t-SNE overlay

t-SNE projection highlighting cluster-specific enrichment patterns.

Pseudobulk expression profiles

Heatmap of pseudobulked expressions of cell-type across clusters.

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Open the notebooks above to reproduce analyses and regenerate figures. Contact the authors for questions or data access.