Augusta 1.0.5
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Description:
Augusta 1.0.5
Python package: From RNA-Seq to the Boolean Network through the Gene Regulatory Network
Documentation and tutorials are available at 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.
$ 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)
License:
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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