Package to perform enrichment analysis in python using EnrichR and OpenTargets APIs
Project description
Enrich_Omics: A Python wrapper for EnrichR and OpenTargets
Table of Contents
About
Python wrapper for EnrichR and OpenTargets API. Allows for visualisation of enriched pathways or disease 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 with enrichment results ans 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
Drug endpoint
- Get drug description
- Get a table with drug information (year of approval, drug type, toxicity, warnings)
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
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'])
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)
Contributions always welcome!
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
enrich_omics-0.1.6.tar.gz
(6.5 kB
view hashes)
Built Distribution
Close
Hashes for enrich_omics-0.1.6-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 1eab8bedf341b4e46350655eb33f0c11a11662191fce3f78ecb312cf3ea71abc |
|
MD5 | 354aaa6e8169f67a4b70c10313b9dadb |
|
BLAKE2b-256 | 7255a0686bd7efa1b1b46494fd8b99c932a5a89cfa8d95114c387c8358f7c001 |