.. _WAD Documentation:


WAD Documentation
=================

.. image:: https://img.shields.io/badge/license-MIT-green
   :alt: License

`WAD <https://github.com/chae-jh/WAD/tree/main>`_ is a linear programming method for L1-minimal reconstruction loss in wavelet-ATAC data deconvolution.

.. image:: ../WAD_pipeline.png
   :alt: WAD_pipeline
   :width: 600px
   :align: center


Usage
-----

**Input**

- single-cell ATAC reference with defined cell types
- bulk tissue samples for deconvolution

**Output**

- deconvolution_results.tsv

**Example Execution**

::

    WAD \
    --scATAC sample1_celltypeA.bw --cell_type celltypeA \
    --scATAC sample1_celltypeB.bw --cell_type celltypeB \
    --scATAC sample1_celltypeC.bw --cell_type celltypeC \
    --scATAC sample2_celltypeA.bw --cell_type celltypeA \
    --scATAC sample2_celltypeB.bw --cell_type celltypeB \
    --scATAC sample2_celltypeC.bw --cell_type celltypeC \
    --bulk_tissue bulk_sample1.bw \
    --bulk_tissue bulk_sample2.bw \
    --chrom_sizes hg38.chrom.sizes \
    --output_dir deconvolution_results

**Example Output**

::

    BulkSample      CellTypeA       CellTypeB       CellTypeC
    bulk_sample1       40%             50%             10%
    bulk_sample2       35%             50%             15%


Installation
------------

**PyPI / Pip**

WAD can be installed from PyPI using pip:

::

    pip install WAD

We recommend installing using a conda environment:

::

    conda create -n WAD_env
    conda activate WAD_env
    conda install pip
    pip install WAD


Requirements
------------

The list of package version requirements is available in ``setup.py``.

::

    - python == 3.12.7
    - numpy >2.0, <2.3
    - pandas == 2.3.1
    - pyBigWig == 0.3.24
    - PyWavelets == 1.7.0
    - click == 8.1.7
    - scipy == 1.13.1
    - cvxpy == 1.6.6
    - ortools >=9.10, <9.12
    - pyarrow == 20.0.0


License
-------

WAD is released under an `MIT license <https://github.com/chae-jh/WAD/blob/main/LICENSE>`_.



.. toctree::
   :maxdepth: 2
   :caption: API Reference

   WAD.wavelet
   WAD.processing
   WAD.rocco
   WAD.io
   WAD.matrix
   WAD.linear_programming