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PyGenePlexus: a Python package for gene discovery using network-based machine learning
SUMMARY: PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest through a molecular interaction network informed supervised machine learning model. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offe...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900208/ https://www.ncbi.nlm.nih.gov/pubmed/36721325 http://dx.doi.org/10.1093/bioinformatics/btad064 |
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author | Mancuso, Christopher A Liu, Renming Krishnan, Arjun |
author_facet | Mancuso, Christopher A Liu, Renming Krishnan, Arjun |
author_sort | Mancuso, Christopher A |
collection | PubMed |
description | SUMMARY: PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest through a molecular interaction network informed supervised machine learning model. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes. AVAILABILITY AND IMPLEMENTATION: https://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-9900208 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-99002082023-02-07 PyGenePlexus: a Python package for gene discovery using network-based machine learning Mancuso, Christopher A Liu, Renming Krishnan, Arjun Bioinformatics Applications Note SUMMARY: PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest through a molecular interaction network informed supervised machine learning model. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes. AVAILABILITY AND IMPLEMENTATION: https://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2023-01-31 /pmc/articles/PMC9900208/ /pubmed/36721325 http://dx.doi.org/10.1093/bioinformatics/btad064 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Mancuso, Christopher A Liu, Renming Krishnan, Arjun PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title | PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title_full | PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title_fullStr | PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title_full_unstemmed | PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title_short | PyGenePlexus: a Python package for gene discovery using network-based machine learning |
title_sort | pygeneplexus: a python package for gene discovery using network-based machine learning |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900208/ https://www.ncbi.nlm.nih.gov/pubmed/36721325 http://dx.doi.org/10.1093/bioinformatics/btad064 |
work_keys_str_mv | AT mancusochristophera pygeneplexusapythonpackageforgenediscoveryusingnetworkbasedmachinelearning AT liurenming pygeneplexusapythonpackageforgenediscoveryusingnetworkbasedmachinelearning AT krishnanarjun pygeneplexusapythonpackageforgenediscoveryusingnetworkbasedmachinelearning |