Notebooks for reproducing all figures and analysis in the The Specious Art of Single-Cell Genomics preprint.
Where possible, analysis notebooks (.ipynb) are provided that can be run from Google Colab. Colab links are included in every notebook. Just click on the 
An intro to using Colab can be found here. Briefly, run each code cell by selecting the cell and executing Command/Ctrl+Enter. Code cells can be edited by simply clicking on the cell to start typing.
All saved/processed data used for analysis is streamed to the notebooks from CaltechData.
Github for Picasso Algorithm: Provides examples for running Picasso on matrices.
Github for MCML Package: Package for running MCML algorithms and quantitative analysis on labeled data/matrices.
- notebooks
- Picasso and MCML analysis notebooks from which Figures were generated for each dataset used.
- scripts
- Python scripts for MCML and Picasso algorithms.
- Python scripts for quantitative analysis of inter-/intra-distances and KNN metrics.
- data
- Saved analyses outputs (csv).
- env
- Conda environments (yml) for MACOS and Linux. Replicates Colab environment.
- figures
- Figures generated for Supplementary Figure 1 (PCA of simplices).