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scRNA2BoNI - scRNAseq data to Boolean Network Inference

scRNA2BoNI is a general framework to infer Boolean networks from scRNAseq data.

scRNA2BoNI_framework

The framework searches to compute families of Boolean networks that are compatible with scRNAseq data and with prior regulatory knowledge. It is composed of three main steps:

  1. The PKN reconstruction.
  2. The experimental design construction.
  3. The BNs inference.

Prerequisites

scRNABoNI only works under Python 3.8. Two submodules, included in the scRNA2BoNI package, are required:

Installation

  1. Clone the repository including submodules.

    • git clone --recursive git@github.com:mathieubolteau/scRNA2BoNI.git

  2. Install anaconda/miniconda to create virtual env.

  3. Create a virtual env, under Python 3.8.

    • conda create -y --name scRNABoNI_env python==3.8

  4. Activate your virtual env.

    • conda activate scRNABoNI_env

  5. Install scRNA2BoNI, submodules and requirements.

    cd scRNA2BoNI
pip install ./scRNA2BoNI/pyBRAvo/.                 # Install pyBRAvo 
pip install -r ./scRNA2BoNI/caspo/requirements.txt # Install Caspo requirements
pip install ./scRNA2BoNI/caspo/.                   # Install Caspo
pip install .                                      # Install scRNA2BoNI

  6. Verify that scRNA2BoNI is installed

    • scRNA2BoNI --help

Usage

scRNA2BoNI --help
usage: scRNA2BoNI [-h] [--pkn-construction] [--preprocessing]
                  [--pseudo-perturbation-inference] [--bns-inference]
                  configuration_file

positional arguments:
  configuration_file    configuration file path

optional arguments:
  -h, --help            show this help message and exit
  --pkn-construction    run the PKN construction
  --preprocessing       run the preprocessing step
  --pseudo-perturbation-inference
                        run the pseudo-perturbations inference
  --bns-inference       run the BNs inference

scRNA2BoNI works with a configuration file to fix the parameters of each step of the framework.

To make the PKN reconstruction step run the following command:

scRNA2BoNI --pkn-construction --preprocessing <CONFIG FILE>

To make the Experiemental design construction run the following command. Notice that step required that the previous step has already been completed.

scRNA2BoNI --pseudo-perturbation-inference <CONFIG_FILE>

To make the BNs inference step, run the following command:

scRNA2BoNI --bns-inference <CONFIG_FILE>

Demo

In the demo folder, a toy dataset to test the installation of scRNA2BoNI and see the expected results for this toy dataset.

To reproduce the expected results, using the configuration file present in the demo/data folder, run the following steps.

  1. Modify paths in the demo_config.ini file. See PATHS, DATA and PKN CONSTRUCTION sections.

  2. Run the following command:

scRNA2BoNI --pkn-construction --preprocessing --pseudo-perturbation-inference --bns-inference <YOUR_PATH>/scRNA2BoNI/demo/data/demo_config.ini

The execution should take 3/4 minutes.

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