Metadata-Version: 2.1
Name: enrich_omics
Version: 0.1.1
Summary: Package to perform enrichment analysis in python using EnrichR and OpenTargets APIs
Home-page: UNKNOWN
Author: Sara Masarone
License: UNKNOWN
Description: # Enrich_Omics: A Python wrapper for EnrichR and OpenTargets
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         [![License](https://img.shields.io/badge/license-MIT-blue.svg)](/LICENSE)
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        ## Table of Contents
        - [About](#about)
        - [Installation](#installation)
        - [Tutorial](#tutorial)
        
        ## About <a name = "about"></a>
        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 <a name = "installation"></a>
        ```python
        
        pip install enrich-omics
        
        ```
        
        ## Tutorial <a name="tutorial"></a>
        ### EnrichR API
        ``` python
        import enrich_omics
        from enrich_omics import EnrichR
        from enrich_omics import OpenTarget
        
        # 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)
        ```
        ![image](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/Plot_enrichment.png)
        
        ```python
        # specifying a different library
        EnrichR.plot_enrichment(gene_list, library_name = 'BioPlanet_2019')
        ```
        ![image](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/Plot_enrichment2.png)
        ```python
        # get results as table for downstream analysis/ pipeline integration
        EnrichR.get_table_enrichment(['LMNA', 'MYH7', 'TNNT2', 'ACE2'])
        ```
        ![image](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/Get_table_enrichment.png)
        
        ### Open Targets API (Open Targets currently only supports single target enrichment. More information on the OpenTargets website)
        ```python
        # 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](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/Plot_diseases.png)
        
        ```python
        OpenTargets.get_table_drugs(target_id = 'PLG', entrez = True)
        ```
        ![image](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/Get_table_drugs.png)
        
        ```python
        # Plot drugs and diseases associated to a given target
        OpenTargets.plot_drugs_disease(target_id = 'PLG', entrez = True)
        ```
        ![image](https://raw.githubusercontent.com/saramasarone/enrich_omics/main/Pictures/PLot_drug_disease.png)
        
        
        
        Contributions always welcome!
        
        
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
