References
----------

.. [Soldatov19] Soldatov *et al.* (2019),
   *Spatiotemporal structure of cell fate decisions in murine neural crest*,
   `Science <https://doi.org/10.1126/science.aas9536>`__.

.. [Wolf18] Wolf *et al.* (2018),
   *Scanpy: large-scale single-cell gene expression data analysis*,
   `Genome Biology <https://doi.org/10.1186/s13059-017-1382-0>`__.

.. [Setty19] Setty *et al.* (2019),
   *Characterization of cell fate probabilities in single-cell data with Palantir*,
   `Nature Biotechnology <https://doi.org/10.1038/s41587-019-0068-4>`__.

.. [Albergante20] Albergante *et al.* (2019),
   *Robust and Scalable Learning of Complex Intrinsic Dataset Geometry via ElPiGraph*,
   `Entropy <https://doi.org/10.3390/e22030296>`__.

.. [Faure20] Faure *et al.* (2020),
   *Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates*,
   `Nature Communications <https://doi.org/10.1038/s41467-020-17929-4>`__.

.. [Mao15] Mao *et al.* (2015),
   *SimplePPT: A simple principal tree algorithm*,
   `SIAM International Conference on Data Mining <https://doi.org/10.1137/1.9781611974010.89>`__.

.. [Bargaje17] Bargaje *et al. (2017)*,
    *Cell population structure prior to bifurcation predicts efficiency of directed differentiation in human induced pluripotent cells*,
    `PNAS <https://doi.org/10.1073/pnas.1621412114>`__.

.. [Lange22] Lange *et al. (2022)*,
    *CellRank for directed single-cell fate mapping*,
    `Nature Methods <https://doi.org/10.1038/s41592-021-01346-6>`__.

.. [Kameneva21] Kameneva *et al. (2021)*
    *Single-cell transcriptomics of human embryos identifies multiple sympathoblast lineages with potential implications for neuroblastoma origin*,
    `Nature Genetics <https://www.nature.com/articles/s41588-021-00818-x>`__.

.. [Ji22] Ji *et al. (2022)*
    *A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples*,
    `biorxiv <https://doi.org/10.1101/2021.07.10.451910>`__.

.. image:: _static/scFates_logo_dark.png
   :width: 1%
