Single-cell RNA-seq and ATAC-seq integration
============================================

Information on joint gene expression and open chromatin profiling `can be found here <https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression/>`_.

Different datasets are covered:

- 10k peripheral blood mononuclear cells (PBMCs) (data by 10x Genomics can be found `here <https://support.10xgenomics.com/single-cell-multiome-atac-gex/datasets/1.0.0/pbmc_granulocyte_sorted_10k>`_):

	
	1. `gene expression processing notebooks <pbmc10k/1-Gene-Expression-Processing.ipynb>`_ — largely follows `this scanpy tutorial <https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html>`_ on processing and clustering PBMCs;

	2. `peaks processing notebook <pbmc10k/2-Chromatin-Accessibility-Processing.ipynb>`_ introduces ATAC-related functionality for data processing and visualisation,

	3. `multimodal omics data integration notebook <pbmc10k/3-Multimodal-Omics-Data-Integration.ipynb>`_ demonstrates how multiple modalities can be combined in a single Python workflow and how multi-omics methods such as `multi-omics factor analysis (MOFA) <https://biofam.github.io/MOFA2/>`_ can be applied for data analysis and interpretation.
    
- 3k cells from the frozen human healthy brain tissue (data by 10x Genomics can be found `here <https://www.10xgenomics.com/resources/datasets/frozen-human-healthy-brain-tissue-3-k-1-standard-2-0-0>`_):

    4. `processing individual modalities and multi-omics integration <brain3k/1-Processing-and-Integration.ipynb>`_ demonstrates how individual modalities can be processed and integrated to prepare the ground for downstream analysis,
    
    4. `celltype annotation <brain3k/2-Celltype-Annotation.ipynb>`_ offers a closer look at how cell type labels can be assigned with a few complementary approaches.


.. toctree::
   :hidden:
   :maxdepth: 3

   pbmc10k/1-Gene-Expression-Processing.ipynb
   pbmc10k/2-Chromatin-Accessibility-Processing.ipynb
   pbmc10k/3-Multimodal-Omics-Data-Integration.ipynb
   brain3k/1-Processing-and-Integration.ipynb
   brain3k/2-Celltype-Annotation.ipynb