This repository contains analysis scripts for the manuscript Single-nucleus transcriptomics reveals cell type-specific and time-dependent effects of psilocybin and ketamine on gene expression by Liao, O'Farrell, Weiner et al, 2026.
This study is a collaboration between
- the Alex Kwan lab at Cornell University (Meinig School of Biomedical Engineering)
- the Kenneth Kwan lab at University of Michigan (Michigan Neuroscience Institue, Department of Human Genetics)
Data that has been processed and analyzed by the authors is available at https://doi.org/10.5281/zenodo.19666128. This includes
- AnnData h5ad file with log(CPM) and raw counts (12.3 GB)
- pseudobulk differential expression sqlite database (1.6 GB)
Raw fastq files can be downloaded from the SRA Accession.
Per cellranger v7.1.0 docs, each sample should be in its own directory entitled with the sample name (ie. 4797-CL-1/)
Files split into different sequencing lanes should be concatenated.
(Note that the 4 samples requiring concatenation were all excluded from the analysis due to oversequencing).
Processing should follow the Methods section of the manuscript.
The provided Snakefile can be used as a template but was built specifically for the authors' file system.
Loading the matrices, quality control and preprocessing, transformations, UMAP embeddings, and clustering can be found in the analysis folder. This also includes differential expression analysis with pyDESeq2.
Code to generate figures appearing in the paper and supplement can be found in the paper_figures folder. This should be run only after running scripts in analysis
Please refer to manuscript for correspondance details