Notebooks utilized to produce results for the publication "Innate immune response to AAV-based gene therapy vectors: mechanisms of complement activation and cytokine release"
- Standard workflow (adapted from besca 2.5, based on scanpy; with and without batch correction)
- Cell annotation workflow (adapted from besca 2.5, based on scanpy, including exploratory analyses related to signature and marker gene expression; with and without batch correction)
- Differential expression notebooks (export of pseudobulk profiles and exploratory DE analysis at single-cell level; 3 version, complete and stratified per IFN subclass) and Rmd files (in pseudobulk folder) The underlying count data and processed and annotated .h5ad can be retrieved from ArrayExpress, accession nr. E-MTAB-14760