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scFates - a python package for advanced pseudotime and bifurcation analysis
===========================================================================

**scFates** is a scalable Python suite for tree inference and advanced pseudotime analysis.



The related work is now available in Bioinformatics_::

    Louis Faure, Ruslan Soldatov, Peter V. Kharchenko, Igor Adameyko
    scFates: a scalable python package for advanced pseudotime and bifurcation analysis from single cell data
    Bioinformatics, btac746; doi: https://doi.org/10.1093/bioinformatics/btac746


It initially is a translation from crestree_, a R package developed for the analysis of neural crest fates during
murine embryonic development (`Soldatov et al., Science, 2019 <https://doi.org/10.1126/science.aas9536>`_), and used
in another study of neural crest derived sensory neurons (`Faure et al., Nature Communications, 2020 <https://doi.org/10.1038/s41467-020-17929-4>`_).

The initial R version included a tree inference approach inspired from SimplePPT, this version now adds the choice of using ElPiGraph_,
another method for principal graph learning (`Albergante et al., Entropy, 2020 <https://doi.org/10.3390/e22030296>`_).
scFates is fully compatible with scanpy_, and contains GPU-accelerated functions for faster and scalable inference.


Analysis key steps
^^^^^^^^^^^^^^^^^^
- learn a principal tree on the space of your choice (gene expression, PCA, diffusion, ...).
- obtain a pseudotime value upon selection of a root (or two roots).
- test and fit features significantly changing along the tree, cluster them.
- perform differential expression between branches.
- identify branch-specific early activating features and probe their correlations prior to bifurcation.

.. toctree::
   :caption: Main
   :maxdepth: 2
   :hidden:

   installation
   api
   release_notes
   references

.. toctree::
   :caption: Walkthroughs
   :maxdepth: 2
   :hidden:

   Basic_Curved_trajectory_analysis
   Tree_Analysis_Bone_marrow_fates
   Tree_operations
   Explore_sigma
   Conversion_from_CellRank_pipeline
   Beyond_scRNAseq

.. _scanpy: https://scanpy.readthedocs.io/
.. _crestree: https://github.com/hms-dbmi/crestree
.. _ElPiGraph: https://github.com/j-bac/elpigraph-python/
.. _Bioinformatics: https://doi.org/10.1093/bioinformatics/btac746