pyMultiOmics

A Python package for multi-omics data integration and analysis


Keywords
machine-learning, bioinformatics, data-integration, proteomics, metabolomics, transcriptomics, multi-omics
License
MIT
Install
pip install pyMultiOmics==1.0.0

Documentation

pyMultiOmics

pyMultiOmics is a Python package for multi-omics data integration and analysis. It uses the Reactome database to map entities (genes, transcripts, proteins, compounds) to their reactions and pathways. The results is then shown as a network graph. Various analyses such as differential analysis, pathway activity analysis can be performed on this network graph, with the results overlaid on the graph.

Installation

Simply run:

pip install pyMultiOmics

Usage

Example basic usage is shown below:

from pyWebOmics.mapping import Mapper

species_name = DANIO_RERIO
m = Mapper(species_name) \
        .set_gene(gene_data, gene_design) \
        .set_protein(protein_data, protein_design) \
        .set_compound(compound_data, compound_design) \
        .build()

m contains a mapper object, which can be interogated to obtain the data integration results. Please refer to this notebook for a demo.