stringdb 0.1.5

Python functions to access the STRING API, a source of protein-protein association networks.

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.