Augusta 1.0.5

Python package for inference of the gene regulatory network and the boolean network using RNA-Seq data.

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)