Enrichr
Perform an enrichment analysis on a list of genes using Enrichr.
This requires at minimum a database name (listed here) and any number of gene symbols to perform enrichment analysis on.
Library Shorthands
Some shorthands for the library are built into the program for convenience. These can be used in the command line interface or in the python interface.
| Alias | Library |
|---|---|
| pathway | KEGG_2021_Human |
| transcription | ChEA_2016 |
| ontology | GO_Biological_Processes_2021 |
| diseases_drugs | GWAS_Catalog_2019 |
| celltypes | PangloaDB_Augmented_2021 |
| kinase_interactions | KEA_2015 |
Arguments
| Name | Short | Long | Description |
|---|---|---|---|
| Library | -l | --library | a library shorthand or any Enrichr library |
| Output | -o | --output | optional filepath to write output to [default=stdout] |
Command Line Interface
# Perform an enrichment analysis using Enrichr
ggetrs enrichr enrichr -l GO_Biological_Process_2021 AP2S1 NSD1 RFX3
# Perform an enrichment analysis with a shorthand library
# this is equivalent to the above search
ggetrs enrichr enrichr -l ontology AP2S1 NSD1 RFX3
# Perform an enrichment analysis on pathway
ggetrs enrichr enrichr -l pathway AP2S1 NSD1 RFX3
Python
import ggetrs
# Search using the ontology shorthand
ggetrs.enrichr("ontology", ["AP2S1", "RFX3", "NSD1"])
# Search using the kinase_interactions shorthand
ggetrs.enrichr("kinase_interactions", ["AP2S1", "RFX3", "NSD1"])