Welcome to Compass’s documentation!

Compass is an algorithm to characterize the metabolic state of cells based on single-cell RNA-Seq and flux balance analysis (FBA). Its development was motivated by the challenge in characterizing the metabolic states of single cells on scale with current metabolic assays. Compass is an in silico approach to infer metabolic status of cells based on transcriptome data, which is readily available even in single cell resolutions.

For a detailed description of the algorithm, refer to Wagner et al., Cell 2021 (link). Code is available on our lab’s GitHub page (link).

These pages have guides on how to install and use Compass, including a walkthrough of an analysis to replicate figures from the manuscript.