========================
Tutorials
========================

Input
=====

- **cell_feature_matrix.h5**

  An HDF5 file containing the gene expression count matrix generated by the sequencing pipeline.
  The matrix stores the number of transcripts detected for each gene (features) in each cell or spot.
  It also includes metadata such as feature IDs, feature names, barcodes, and matrix indices in a compressed sparse format.

- **cells.csv.gz**

  A compressed CSV file containing metadata for each cell or spot.
  This file typically includes cell barcodes and associated attributes such as spatial coordinates,
  quality metrics, or annotation labels produced by the processing pipeline.


Main Features
=============

.. grid:: 1 2 3 3
   :gutter: 3

   .. grid-item-card::
      :link: tutorials/cell_analysis
      :text-align: center

      .. image:: _static/images/cell_analysis.png
         :width: 220px

      **Cell Distribution Clustering**

   .. grid-item-card::
      :link: tutorials/gene_analysis
      :text-align: center

      .. image:: _static/images/gene_analysis.png
         :width: 220px

      **Gene Distribution Clustering**

   .. grid-item-card::
      :link: tutorials/spatial_deg
      :text-align: center

      .. image:: _static/images/spatial_deg.png
         :width: 220px

      **Spatially DEG analysis**