Contains the following files:
- Quality control R markdown file containing code for Quality Control of the Lo Giudice et al. (2020) dataset
- Metadata R markdown file containing code for splitting Lo Giudice et al. (2020) dataset to Lane 1 only and adding various attributes to the gene and cell metadata. This included CytoTRACE score, CellAssign cell type annotations, Cell Cycle Phase Annotations, Gene types and Highly Variable Gene selections.
- scRNA-seq simulation and cross-validation Python file. Until the simulation overview, the code in this file comes from the simulate_example_data.ipynb contained in the GitHub Repository: https://github.com/dylkot/cNMF/tree/master/Extras.
- Cross-validation Python file for the Lo Giudice et al. (2020) dataset.
- NMF Biological Interpretation Python file for the Lo Giudice et al. (2020) dataset, detailing the analysis to interpret the results of NMF.
- Project writeup document containing the full details of all the above analyses.