/enrich_omics

A python package to explore pathways, diseases and drugs associated to a list of targets (genes, proteins, etc)

Primary LanguagePythonMIT LicenseMIT

EnrichOmics: A Python wrapper for EnrichR and OpenTargets

Status License GitHub Issues GitHub Pull Requests

Table of contents

About

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

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)

image

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

image

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

image

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)

image

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

image

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

image

Docs

Documentation for this package can be found here

Contributions always welcome!