stringdb
Python functions to access the STRINGdb API, a source of protein-protein association networks. Documentation for the api can be found here: https://string-db.org/help/api/
Free software: MIT license
Documentation: https://stringdb.readthedocs.io.
Tutorial
To install:
$ pip install stringdb
Basic Usage
import stringdb genes = ['TP53', 'BRCA1', 'FANCD1', 'FANCL'] string_ids = stringdb.get_string_ids(genes) enrichment_df = stringdb.get_enrichment(string_ids.queryItem)
There are 5 functions for querying a list of stringIds, which follow the pattern get_*
where * can be ‘enrichment’, ‘interaction_partners’, ‘ppi_enrichment’, ‘network’, and ‘functional_annotation’
TODO
Credits
This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.
History
0.1.5 (2020-08-18)
Allow for background identifiers in enrichment analysis
0.1.4 - 0.1.2 (2020-06-24)
Setup travis pypi release
0.1.1 (2020-06-24)
Added requests to requirements
0.1.0 (2020-06-22)
First release on PyPI.
4 maintainers
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