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Welcome to CWAS-Plus2 documentation!
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CWAS-Plus2 (Category-Wide Association Study) is a data analysis tool designed to conduct rigorous association tests for discovering noncoding associations in complex genomic disorders. It runs category-based burden tests using variants from whole-genome sequencing data and various annotation datasets. CWAS-Plus2 provides a user-friendly interface for efficient hypothesis testing and has promising implications for uncovering the pathophysiology of various genomic disorders.

Here are the reference papers:

* `An analytical framework for whole genome sequence association studies and its implications for autism spectrum disorder <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961723/>`_ (Werling et al., 2018)
* `Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6432922/>`_ (An et al., 2018)
* `CWAS-Plus: Estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data <https://pubmed.ncbi.nlm.nih.gov/38966948/>`_ (Kim et al., 2024)


CWAS-Plus2 workflow
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.. figure:: ../images/CWAS_workflow.jpg
   :alt: CWAS-Plus2 workflow
   :width: 90%
   :align: center

   **A.** Workflow\: Variants extracted from whole-genome sequencing data of samples (sample variant) serve as inputs. **B-G.** Graphic descriptions of each process in CWAS-Plus2\: Red (case) and blue (control) represent the phenotype. **F.** Representative network pointed by the purple arrow provides an enlarged view of a subset of the network. Node color indicates the direction of the burden in each category (red, case burden; blue, control burden). **G.** Node color reflects the scale of the normalized z-score, which represents the degree of disease association of the cluster. Darker red indicates a higher association. Node size represents the number of categories within the cluster.


.. toctree::
   :maxdepth: 1
   :caption: CWAS-Plus2 tutorial

   quickstart/quick_tutorial.rst
   quickstart/advanced_tutorial.rst

.. toctree::
   :maxdepth: 1
   :caption: CWAS-Plus2 installation

   install/installation.rst

.. toctree::
   :maxdepth: 1
   :caption: CWAS-Plus2 requirements

   required/input.rst
   required/annotations.rst

.. toctree::
   :maxdepth: 1
   :caption: CWAS-Plus2 configuration

   config/configuration.rst

.. toctree::
   :maxdepth: 1
   :caption: CWAS-Plus2 steps

   steps/annotation.rst
   steps/categorization.rst
   steps/burden.rst
   steps/correlation.rst
   steps/effective_num_test.rst
   steps/risk_score.rst
   steps/burdenshift.rst
   steps/dawn.rst

.. toctree::
   :maxdepth: 1
   :caption: Other useful commands

   utils/extract_variants.rst

.. toctree::
   :maxdepth: 1
   :caption: FAQ

   faq/faq.rst

Misc.
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Here is the original CWAS repository: `sanderslab/cwas <https://github.com/sanderslab/cwas>`_