.. RISE documentation master file

Welcome to RISE's documentation!
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Overview
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RISE (Reduction and Insight in Single-cell Exploration) is an unsupervised, tensor-based computational method designed for the integrative analysis of single-cell RNA sequencing (scRNA-seq) data across multiple experimental conditions, such as drug treatments, patient cohorts, or time points. Built upon the PARAFAC2 tensor decomposition framework, 
RISE preserves the inherent three-dimensional structure of multi-condition single-cell data—conditions x cells x genes—instead of flattening it into a conventional two-dimensional matrix. This allows RISE to decompose variation into distinct, interpretable patterns associated with experimental conditions, individual cells, and genes, providing a 
more nuanced and biologically meaningful analysis. 

RISE does not require prior cell-type labels or clustering, reducing bias and enabling discovery of novel cell states, while also separating technical, biological, and condition-driven variation without  batch correction that may erase meaningful signals. 
Its high resolution enables the identification of cell populations and condition-specific subpopulations missed by pseudobulk or clustering-based approaches, and each resulting component is directly linked to specific conditions, genes, and cells, making the results biologically tractable.

.. toctree::
   :maxdepth: 1
   :caption: Contents:

   tutorial
   api
   references

Indices and tables
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* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

.. Updated December 2025