Metabolism is a major regulator of immune cell function, but it remains difficult to study the metabolic status of individual cells. This motivated the development of Compass, an algorithm to characterize cellular metabolic states based on single-cell RNA-Seq and flux balance analysis (FBA).
For instructions on how to install and use Compass, visit the documentation. For a detailed description of the algorithm, refer to the biorxiv preprints (manuscript1, manuscript2).
This branch of our Github repo is focused on post-processing/analysis of the results of Compass and demonstrates this with a jupyter notebook and example Th17 data. To download the code, you can clone the repo with:
git clone https://github.com/YosefLab/Compass.gitAlternatively, all of the files can be downloaded as a zip file from Github's user interface (click the green Code button and then Download Zip). Then the jupyter notebook can be run in the same way as other jupyter notebooks.