EpiTrace - Estimating cell age from single-cell ATAC data
=========================================================

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**EpiTrace** is an R package for estimating cell age from single-cell ATAC-seq data. It takes an approximation approach to infer the relative mitosis (replicative) age -- the number of mitosis a cell has undergone. It does so by measuring the total opened reference "clock-like" genomic loci. On these loci, heterogeneity of chromatin accessibility decreases as the cell ages. The chromatin accessibility-based mitosis age inferred by EpiTrace adds a time domain to the single-cell sequencing data. It complements somatic mutation, RNA velocity and stemness predictions to predict the cell evolution trajectory with improved precision and power :cite:p:`Xiao2024`. 






EpiTrace's key applications
---------------------------
- estimate the mitosis age of single cell or bulk sample.  
- identify age-dependent biological events including shifts in chromatin accessibility, transcription factor activity, and transcriptomic changes. 
- timing developmental and mutational events. 



Citing EpiTrace
---------------

If you include or rely on EpiTrace when publishing research, please adhere to the
following citation guide:

**EpiTrace algorithm and the ClockDML**

If you use the *algorithm* and/or *ClockDML* (*clock-like differential methylated loci*), including cross-species lift-over clock-like loci generated from the ClockDML, cite

.. code-block:: bibtex

    @article {Xiao2024,
	author = {Xiao, Yu and Jin, Wan and Ju, Lingao and Fu, Jie and Wang, Gang and Yu, Mengxue and Chen, Fangjin and Qian, Kaiyu and Wang, Xinghuan and Zhang, Yi},
	title = {Tracking single-cell evolution using clock-like chromatin accessibility loci},
	year = {2024},
	doi = {10.1038/s41587-024-02241-z},
	URL = {https://doi.org/10.1038/s41587-024-02241-z},
	journal = {Nat Biotech}}


**G-quadruplex region**

If you use the *G-quadruplex region* for cell/sample age estimation, cite

.. code-block:: bibtex

    @article {Jin2024.01.06.574476,
	author = {Wan Jin and Jing Zheng and Yu Xiao and Lingao Ju and Fangjin Chen and Jie Fu and Hui Jiang and Yi Zhang},
	title = {A universal molecular mechanism driving aging},
	elocation-id = {2024.01.06.574476},
	year = {2024},
	doi = {10.1101/2024.01.06.574476},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2024/01/06/2024.01.06.574476},
	eprint = {https://www.biorxiv.org/content/early/2024/01/06/2024.01.06.574476.full.pdf},
	journal = {bioRxiv}}



Support
-------
Have a question or would like to start a new discussion? Found a bug or would like to see a feature implemented? Feel free to submit an
`issue <https://github.com/MagpiePKU/EpiTrace/issues/new>`_.
Your help to improve EpiTrace is highly appreciated. 


Planned updates
---------------
Tutorial on (1) using G-quadruplex as reference clock-like loci, and (2) timing mutational event during oncogenesis.     


.. toctree::
   :caption: Main
   :maxdepth: 1
   :hidden:

   about
   installation
   release_notes
   interpreting_epitrace_age
   clock_reference_options
   using_notes
   references


.. toctree::
   :caption: Tutorials
   :maxdepth: 1
   :hidden:

   tutorial_overview
   Bulk_ATAC
   scATAC_cIPSC
   MSscATAC
   scATAC_drosophila
   mtscATAC_CD34


.. toctree::
   :caption: Functions
   :maxdepth: 1
   :hidden:

   Init_Peakset 
   Init_Matrix
   EpiTrace_prepare_object
   EpiTraceAge
   RunEpiTraceAge
   EpiTraceAge_Convergence
   AssociationOfPeaksToAge
   RunEpiTracePhylogeny





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