2024 updated single-cell guide - Part 2: RNA Integration and annotation

In this video I integrate the single-cell RNA data together with scVI and use multiple methods of label transfer from reference datasets. I then verify and annotate the individual clusters using known marker genes. This video covers advanced analysis steps, such as tuning hyperparameters in our scVI model, making custom reference datasets, and more. Main notebook: https://github.com/mousepixels/sanbomics_scripts/blob/main/sc2024/annotation_integration.ipynb Example of bad mapping: https://github.com/mousepixels/sanbomics_scripts/blob/main/sc2024/bad_mapping.ipynb Part 1: https://youtu.be/cmOlCTGX4Ik 0:00 Celltypist transfer 13:49 scVI transfer 21:13 Integration 29:22 Dim reduction 34:00 Annotation