.. multiome-wf documentation master file, created by
   sphinx-quickstart on Sun Jan 30 19:22:49 2022.
   You can adapt this file completely to your liking, but it should at least
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.. toctree::
   :caption: Getting Started
   :maxdepth: 1
   :name: getting-started
   :hidden:

   getting-started/setup
   getting-started/tutorial
   getting-started/why-use

.. toctree::
   :caption: Workflows
   :maxdepth: 1
   :name: workflows
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   workflows/overview-wf
   workflows/multiome
   workflows/rna
   workflows/atac
   workflows/overview-input
   workflows/overview-output

.. toctree::
   :caption: Configuration
   :maxdepth: 1
   :name: configuration
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   configuration/config
   configuration/config-yaml
   configuration/samples-table
   configuration/aggregates-table
   configuration/assays-table
   configuration/config-multiome
   configuration/config-rna
   configuration/config-atac

.. toctree::
   :caption: Project Info
   :maxdepth: 1
   :name: project-info
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   project-info/citations
   project-info/faq
   project-info/changelog
   project-info/authors

.. _docs-main:

About
=====

`multiome-wf` is a `Snakemake <https://snakemake.readthedocs.io/en/stable/>`_ 
workflow for common single cell sequencing analyses.

With the advent of new sequencing methods and associated data sets, combining different
single cell sequencing modalities is cumbersome and error-prone. A core feature of the
`multiome-wf` is standardizing how disparate data types are combined and preprocessed
prior to downstream analyses.

The workflow was built around `10X Genomics <https://www.10xgenomics.com/>`_ products, 
but should work with any single cell data set as long as the input matrices have been 
properly formatted.

Some of the modalities this workflow supports include:

- Gene Expression: mapped and quantified by ``cellranger count`` and ``cellranger aggr``

- ATAC: mapped and quantified by ``cellranger-atac count`` and ``cellranger-atac aggr``

- Multiome (Gene Exression + ATAC from same cell), CITE-Seq: mapped and quantified by 
  ``cellranger-arc count`` and ``cellranger-arc aggr``

- Cell Multiplexing (Cell Multiplexing Oligos): demultiplexed using cellranger pipelines.

- Multiple Batches, Multiple experimental conditions

.. note::

    - While this workflow does some basic tertiary analyses, such as differential testing, 
      the core purpose of this workflow is preparing a unified dataset to be used as input 
      for standalone downstream analyses, such as Trajectory Inference, Gene-Peak Interactions,
      etc which are not currently supported by this workflow.

    - Users need familarity with `Snakemake <https://snakemake.readthedocs.io/en/stable/>`_, 
      `Conda <https://conda.io/projects/conda/en/latest/user-guide/getting-started.html>`_, 
      and `Seurat <https://satijalab.org/seurat>`_ for effective use of `multiome-wf`.


Getting Started
---------------

See :ref:`setup` to get started.

See :ref:`overview-wf` to learn more about the supported workflows.