RNACOREX 0.1.5

RNA Coregulation Network Explorer and Classifier

RNACOREX

RNACOREX is a Python package for building Bayesian Network based classification models using miRNA-mRNA post-transcriptional networks. It uses curated interaction databases and conditional mutual information for identifying sets of interactions and model them using Conditional Linear Gaussian Classifiers (CLGs).

Repository: RNACOREX on GitHub

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🚀 Features

• Extracts structural and functional scores from miRNA-mRNA interactions.
• Identify sets of interactions associated with different phenotypes.
• Build CLG classifiers using these interaction sets.
• Display the post-transcriptional networks.

📦 Installation

Installation in a Python virtual environment is required. It is highly recommended to run it in a conda environment.

Install with:

pip install rnacorex

Important: Next engines must be placed in their path rnacorex\engines before running the package.

• DIANA_targets.txt
• Tarbase_v9.tsv
• Targetscan_targets.txt
• MTB_targets_25.txt
• gencode.v47.basic.annotation.gtf

Engines can be downloaded using the next command:

rnacorex.download()

Alternatively they can be manually downloaded from: https://tinyurl.com/RNACOREX

Run the next command to check if the engines have been correctly added:

rnacorex.check_engines()

Important: For displaying networks,pygraphviz must be installed separately using conda:

conda install -c conda-forge pygraphviz