Analysis notebooks

Our analyses and results are described in several Jupyter notebooks, which can be used to generate most of the Figures and Tables in the paper. The analyses are divided into the following notebooks:

1. Tumor morphology (Figure 1)
2. Expression analyses (Figure 2)
3. Insertion analyses (Figure 3)
4. Human relevance (Figure 4)
5. Truncation variants (Figure 5)
6. TIDE analysis (Figure 7)

1. Supplemental Tables
2. Supplemental Figures
3. Figshare dataset

In general, each notebook describes the analysis for a single Figure or set of results. Notebooks A and B contain a number of supplemental analyses that are not included in the other notebooks. The Figshare notebook contains the code that was used to create the dataset shared on Figshare.

Static versions of the notebooks can be viewed in the Github repository.