The code and jupyter notebooks to go along with the manuscript: Comparison of the Cellular and Molecular Atlases of the Macaque and Mouse Dorsal Horns. This github details the analysis performed on single nucleus RNA-seq data sampled from the Rhesus macaque dorsal. The resulting analysis yielded precise gene markers for all neural cell types in the macaque dorsal horn and a comparison of the expression patterns with their homologous mouse cell types. You can follow along the analysis with the Jupyter notebooks below.
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R>4.0.5
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python>3.8.1
The rest of the requirements can be found below:
- python : conda_env.yml
- R: R_installed_packages.csv
The analysis was composed of the following steps and can be viewed in the analysis jupyer notebooks.
| Computational Step | Associated Notebook |
|---|---|
| Empty Droplet Removal | qc_analysis.ipynb |
| Doublet Removal | qc_analysis.ipynb |
| Preclustering | preclustering.ipynb |
| Normalization | normalization.ipynb |
| Biological Replicate Integration | integration_analysis.ipynb |
| Marker Gene Analysis | integration_analysis.ipynb |
| Mouse Comparative Analysis | mouse_comparison.ipynb |
Data will be available via SRA and GEO soon!