.. Autogenerated by build.py


=======================
BPReveal Documentataion
=======================

BPReveal is a suite of tools for working with sequence-to-profile models in the vein of
BPNet.

It incorporates bias correction in the style of chrombpnet-lite, but with added features
to regress out very complex biases.

You can get your own copy of BPReveal from the project's
`GitHub page <https://github.com/mmtrebuchet/bpreveal>`_.

It also incorporates a new interpretation tool, called :doc:`PISA<_generated/pisa>`
(Pairwise Interaction Shap Analysis) that lets you view a two-dimensional map of cause
and effect over a region.

For a summary of the components of BPReveal, see :doc:`Programs<_generated/programs>`.

#ifdef MAN_PAGE

**Man pages**

BPReveal contains a lot of code! This meta-man page contains
all of the documentation, but you can look up the documentation you
need in one of the pages relevant to the program you're using.

Here are the man pages included in BPReveal:

Section 1: MAN_PAGES_SECTION_1

Section 3: MAN_PAGES_SECTION_3

Section 7: MAN_PAGES_SECTION_7

You can use ``man motifScan`` to get documentation on the ``motifScan``
program, for example.

#endif


**Authors**

* Charles McAnany, Ph.D.
* Melanie Weilert
* Haining Jiang
* Patrick Moeller
* Anshul Kundaje, Ph.D.
* Julia Zeitlinger, Ph.D.


**Contact**

The principal contact is Charles McAnany. His Stowers address is cm2363@stowers.org, and
his personal address is bpreveal@charlesmcanany.com.

At Stowers, Melanie Weilert is an excellent resource, she is the staff bioinformatician
in the Zeitlinger lab.

If you're at Stowers and want to use BPReveal for a project, the fine folks in
Computational Biology are familiar with the package and can get you set up.


..
    Copyright 2022, 2023, 2024 Charles McAnany. This file is part of BPReveal. BPReveal is free software: You can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version. BPReveal is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with BPReveal. If not, see <https://www.gnu.org/licenses/>.

.. toctree::
    :maxdepth: 2

    _generated/text
    _generated/majorcli
    _generated/minorcli
    _generated/api
    _generated/toolsminor
    _generated/toolsmajor
    _generated/toolsapi
    _generated/internalapi
    _generated/development

*******
Indices
*******

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`