Metadata-Version: 2.1
Name: Augusta
Version: 1.0.3
Summary: Python package for inference of the gene regulatory network and the boolean network using RNA-Seq data.
Home-page: https://github.com/JanaMus/Augusta
Author: Jana Musilova, Zdenek Vafek, Karel Sedlar
Author-email: musilovajana@vut.cz
License: MIT
Keywords: Computational biology,Bioinformatics,RNA-Seq,mutual information,database,Boolean network,Gene Regulatory network,SBML
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Development Status :: 4 - Beta
Requires-Python: >=3.7, <3.9
License-File: LICENSE

Augusta
==========

Python package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network

Documentation and tutorials are available at `augusta.readthedocs.io <https://augusta.readthedocs.io>`_.

Quick Guide
----------------

Dependencies:

- Python 3, versions 3.7 and 3.8
- Docker

**Installation:**

We highly recomment installing and using Augusta in a virtual environment.

.. code-block::

   $ conda create -n Augusta_venv python=3.7 anaconda
   $ conda activate Augusta_venv
   

.. code-block::

   $ pip install Augusta


**Usage:**

See `Inputs <https://augusta.readthedocs.io/en/latest/User%20guide.html>`_ for details about input files and variables.

.. code-block:: 

   $ python
   >>> import Augusta
   
GRN and BN inference using RNA-Seq:

.. code-block:: 

   >>> Augusta.RNASeq_to_SBML(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string')

GRN inference using RNA-Seq:

.. code-block:: 

   >>> GRN = Augusta.RNASeq_to_GRN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string')


BN inference using GRN:

.. code-block:: 

   >>> Augusta.GRNtoBN(GRN_input = 'MyGRN_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', add_dbs_info = 'My_string')
   



