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Welcome to the Compass 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 <https://doi.org/10.1016/j.cell.2021.05.045>`__). Code is available on our lab's GitHub page (`link <https://github.com/YosefLab/Compass>`__).

These pages have guides on how to install and use Compass, including a walkthrough of an analysis to replicate figures from the manuscript.
   
.. toctree::
   :maxdepth: 1
   :caption: Contents:
   :titlesonly:
   
   installation
   quickstart
   settings
   turbo_compass
   module_compass
   notebooks/postprocessing
   notebooks/pseudobulk
   changelog