wdecoster / enrichr_cli

Python script to use enrichr from command line (http://amp.pharm.mssm.edu/Enrichr/)

enrichr_cli

Python script to query enrichr from command line (http://amp.pharm.mssm.edu/Enrichr/)

Required python libraries:

• json
• requests
• sys
• os

Input

Input is a newline-separated list of gene symbols, either from a file or on stdin.

Usage

• python enrichR.py genelist.txt [using default databases, see further]
• python enrichR.py genelist GO_Molecular_Function_2015 [using just one database]
• python enrichR.py genelist GO_Molecular_Function_2015 Reactome_2016 [using just two databases]
• cat genelist.txt | python enrichR.py - [reading from a pipe]

Output:

Per used database a file will be created containing the enrichment results.

Databases

To get a list of all available databases: python enrichR.py databases

Default databases, used without specifying a database:

• KEGG_2015
• BioCarta_2016
• WikiPathways_2016
• Reactome_2016
• GO_Biological_Process_2015
• GO_Cellular_Component_2015
• GO_Molecular_Function_2015
• MSigDB_Computational
• Panther_2016

Notes

• The databases are hardcoded in the script and as such will not follow updates from Enrichr automatically.
• If you specify a database which is not available you will receive a warning.
• If not a single valid database is specified the default set will be used.

I'm not affiliated to the authors of Enrichr but just use their API.