Shalek Lab How Tos¶
- 1. Reading in the data (to R)
- 2. Dropout?
- 3. Filtering
- 4. Doublets
- 5. Normalization
- 6. Choosing variable genes
- 7. PCA
- 8. Other dimensionality reduction
- 9. Batch Correction
- 10. Imputation
- 11. Clustering
- 12. How do I know I have a good clustering?
- 13. What if I am looking for rare cell subsets?
- 14. What if some cells are clearly placed in the wrong clusters?
- 15. Differential Expression
- 16. Cell Ordering (“Pseudotime”)
- 17. Network Inference
- 18. I have a bunch of genes now what?
- 19. Meta analysis