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>`_.
Credits
----------------
The Augusta project is based on research detailed in the following paper. Please cite this paper when using or referencing our work:
Augusta: From RNA‐Seq to gene regulatory networks and Boolean models. Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomas Helikar, and Karel Sedlar. *Computational and Structural Biotechnology Journal*, 2024. DOI: `10.1016/j.csbj.2024.01.013 <https://doi.org/10.1016/j.csbj.2024.01.013>`_.
Contributors
----------------
- Jana Musilova, musilovaj22@gmail.com
- Zdenek Vafek
- Karel Sedlar, sedlar@vut.cz
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_BN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)
GRN inference using RNA-Seq:
.. code-block::
>>> Augusta.RNASeq_to_GRN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)
BN inference using GRN:
.. code-block::
>>> Augusta.GRN_to_BN(GRN_input = 'MyGRN_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', add_dbs_info = 'My_string')
GRN refinement:
.. code-block::
>>> Augusta.refineGRN(GRN_input = 'MyGRN_file.csv', genbank_file_input = 'MyGB_file.gb', count_table_input = 'MyCT_file.csv', promoter_length = My_number, motifs_max_time = My_seconds)
Raw data
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"description": "Augusta\n==========\n\nPython package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network\n\nDocumentation and tutorials are available at `augusta.readthedocs.io <https://augusta.readthedocs.io>`_.\n\nCredits\n----------------\nThe Augusta project is based on research detailed in the following paper. Please cite this paper when using or referencing our work:\n\nAugusta: From RNA\u2010Seq to gene regulatory networks and Boolean models. Jana Musilova, Zdenek Vafek, Bhanwar Lal Puniya, Ralf Zimmer, Tomas Helikar, and Karel Sedlar. *Computational and Structural Biotechnology Journal*, 2024. DOI: `10.1016/j.csbj.2024.01.013 <https://doi.org/10.1016/j.csbj.2024.01.013>`_.\n\n\nContributors\n----------------\n- Jana Musilova, musilovaj22@gmail.com\n- Zdenek Vafek\n- Karel Sedlar, sedlar@vut.cz\n\n\nQuick Guide\n----------------\n\nDependencies:\n\n- Python 3, versions 3.7 and 3.8\n- Docker\n\n**Installation:**\n\nWe highly recomment installing and using Augusta in a virtual environment.\n\n.. code-block::\n\n $ conda create -n Augusta_venv python=3.7 anaconda\n $ conda activate Augusta_venv\n \n\n.. code-block::\n\n $ pip install Augusta\n\n\n**Usage:** \n\nSee `Inputs <https://augusta.readthedocs.io/en/latest/User%20guide.html>`_ for details about input files and variables.\n\n.. code-block:: \n\n $ python\n >>> import Augusta\n \nGRN and BN inference using RNA-Seq:\n\n.. code-block:: \n\n >>> Augusta.RNASeq_to_BN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)\n\nGRN inference using RNA-Seq:\n\n.. code-block:: \n\n >>> Augusta.RNASeq_to_GRN(count_table_input = 'MyCT_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', normalization_type = 'My_string', motifs_max_time = My_seconds)\n\n\nBN inference using GRN:\n\n.. code-block:: \n\n >>> Augusta.GRN_to_BN(GRN_input = 'MyGRN_file.csv', promoter_length = My_number, genbank_file_input = 'MyGB_file.gb', add_dbs_info = 'My_string')\n\n\nGRN refinement:\n\n.. code-block:: \n\n >>> Augusta.refineGRN(GRN_input = 'MyGRN_file.csv', genbank_file_input = 'MyGB_file.gb', count_table_input = 'MyCT_file.csv', promoter_length = My_number, motifs_max_time = My_seconds)\n\n \n\n\n\n",
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