.. PIASO documentation master file, created by
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PIASO: Precise Integrative Analysis of Single-cell Omics
=====================================================================

Current available functionalities include:

- perform dimensionality reduction with GDR
- integration of scRNA-seq datasets with GDR
- integration of scRNA-seq data and MERFISH/Xenium data with GDR
- normalization of scRNA-seq data with INFOG
- selection of highly-variable genes in scRNA-seq data with INFOG
- a novel gene set scoring method
- run clustering on selected cluster(s)
- side-by-side cell embedding plots, e.g., split by Conditions
- stacked violin plots for multiple features, including genes and cell metrics

Upcoming functionalities:

- preprocessing of scATAC-seq datasets
- integration of scRNA-seq and scATAC-seq datasets (not relying on gene activities)
- inference of cell type-specific gene regulatory networks
and others


Citation
-----------

If PIASO is useful for your research, please consider citing Wu et al., Pyramidal neurons proportionately alter the identity and survival of specific cortical interneuron subtypes, bioRxiv (2024).

.. toctree::
   :maxdepth: 1

   installation
   tutorials
   modules
   references
   releaseNotes


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`
