Reproducible analysis code. Jupyter notebooks have been organized as follows:
- 2021-01-18_curation_ansari - Initial dataset and label curation by Meshal Ansari.
- 2021-01-18_filtered_ansari - Initial preprocessing by Meshal Ansari.
- 2021-01-18_manifold_ansari - Initial batch correction and plotting by Meshal Ansari.
- 2021-01-18_manifold
Patients 1+2, 3, and 4 were sequenced across different runs and thus had moderate batch effect.
- 2021-10-01_scvi_batch_correction
- 2022-01-24_integrate_scanorama - Tried to integrate on the gene expression matrix as well.