enrich-omics

Enrich_Omics: A Python wrapper for EnrichR and OpenTargets

Table of Contents

• About
• Installation
• Tutorial
• Docs

About

Python wrapper for EnrichR and OpenTargets API. Allows for visualisation of enriched pathways or diseases associated to a given target

EnrichR

• Choose from all EnrichR libraries (Transcription, Pathways, Drugs, etc). Default library is KEGG_pathways_2021
• Get table with enrichment results
• Plot enrichment results and export it

OpenTargets

Open Target is currently only supporting the search of a single target

Target endpoint

• Convert Entrez to Ensemble if needed (OpenTargets API accepts only Ensemble IDs)
• Get description of the function of the target
• Get diseases associated to a certain target
• Plot diseases associated to a certain target
• Get table drugs associated to a certain target
• Plot the drugs that work for a given target and the diseases associated to it
• Plot the drugs associated to a given target and the trial phase they are currently in

Plots

• Export plots in SVG and PNG

Installation

pip install enrich-omics

Tutorial

EnrichR API

import enrich_omics
from enrich_omics import EnrichR
from enrich_omics import OpenTargets

# get all available libraries
EnrichR.get_libraries()

# get enrichment for a list of genes/proteins
# default library is 'KEGG_2021_Human' but other libraries can be specified using the 'library_name' argument.
# check out available libraries with the command above
# library_type, height, width and max_hits arguments are optional. See source code for details or docs for examples.

gene_list = ['LMNA', 'MYH7', 'TNNT2', 'ACE2']
EnrichR.plot_enrichment(gene_list)

# specifying a different library
EnrichR.plot_enrichment(gene_list, library_name = 'BioPlanet_2019', height = 200, width = 300, max_hits= None)

# get results as table for downstream analysis/ pipeline integration
EnrichR.get_table_enrichment(['LMNA', 'MYH7', 'TNNT2', 'ACE2'], library_name='KEGG_2021_Human')

Open Targets API (Open Targets currently only supports single target enrichment. More information on the OpenTargets website)

# OpenTargets takes EnsembleIDs by default, but entrez ids can be passed using the argument entrez = True
# Export plots easily in png or svg
OpenTargets.plot_diseases(target_id = 'PLG', entrez = True) 

OpenTargets.get_table_drugs(target_id = 'PLG', entrez = True)

# Plot drugs and diseases associated to a given target
OpenTargets.plot_drugs_disease(target_id = 'PLG', entrez = True)

Docs

Documentation for this package can be found here

Contributions always welcome!