Python package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network
Documentation and tutorials are available at augusta.readthedocs.io.
Dependencies:
- Python 3, versions 3.7 and 3.8
- Docker
Installation:
We highly recomment installing and using Augusta in a virtual environment.
$ conda create -n Augusta_venv python=3.7 anaconda $ conda activate Augusta_venv
$ pip install Augusta
Usage:
See Inputs for details about input files and variables.
$ python >>> import Augusta
GRN and BN inference using RNA-Seq:
>>> 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:
>>> 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:
>>> 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:
>>> 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)
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.
- Jana Musilova
- Zdenek Vafek
- Karel Sedlar