Table 1. User Documentation^a.

Tutorial 1: Data intro	Goes over the basics of how to install the package and access data
Tutorial 2: pandas	More in-depth description of how to work with the tables using pandas
Tutorial 3: Joining DataFrames	Shows how to use built-in functions from cptac to join tables of different data types
Tutorial 4: MultiIndex	Some tables provided by the package use multilevel column indexes in cases where multiple keys are required to uniquely identify each column. This tutorial describes unique aspects of working with these tables
Tutorial 5: Updates	An explanation of how to access and work with data version updates and package version updates
Tutorial 6: Python and R	How access the Python API within R
Use case 1: Multiomic integration	Data access and integration for multiple omics data types
Use case 2: Clinical covariates	Explores metadata for correlation between clinical attributes
Use case 3: Clinical and acetylation	Compares acetylation levels between tumor subtypes
Use case 4: Mutations and omics	Studies the effects of DNA mutations on protein abundance
Use case 5: Enrichment analysis	Uses the GSEApyb module to find enriched pathways
Use case 6: Derived molecular	Identifies correlation between proteomics and attributes derived from molecular data, for example, MSI status
Use case 7: Trans genetic effect	Studies the effect of DNA mutations on the expression of a different protein
Use case 8: Outliers	Uses the Blacksheepc module to study outliers in expression values
Use case 9: Clinical outcomes	Uses patient follow-up data to look for correlations between clinical and molecular data and patient survival
Use case 10: Pathway overlay	Integrates quantitative molecular data with Reactome pathway maps

^aA list of tutorials and use cases to help users explore the data API is available at https://paynelab.github.io/cptac/#documentation.

^bGSEApy module is available at https://gseapy.readthedocs.io/en/latest/introduction.html.

^cBlacksheep module is available at https://blacksheep.readthedocs.io/en/master/.