Tutorials

For beginners, we recommend using the command-line interface (CLI), which automates parts of the workflow and generates many outputs for downstream analysis.

1. CLI factorization <tutorials/cli-factorization.md>

2. CLI integration <tutorials/cli-integration.md>

3. CLI gene set analysis <tutorials/cli-geneset-analysis.md>

For advanced users, we recommend the using Python, which provides better control over the analysis parameters and plotting, as well as integration with other APIs and in-memory data structures. The following tutorials demonstrate how to follow a similar workflow as the CLI tutorials above:

1. Python factorization <tutorials/python-factorization.ipynb>

2. Python integration <tutorials/python-integration.ipynb>

• Command-line interface: Factorization workflow
• Command-line interface: Integration workflow
• Configuring mosaicmpi integrate using a config.toml file
• Command-line interface: Integration workflow
• Python factorization tutorial
• Python integration tutorial