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EPEPT: A web service for enhanced P-value estimation in permutation tests
BACKGROUND: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277916/ https://www.ncbi.nlm.nih.gov/pubmed/22024252 http://dx.doi.org/10.1186/1471-2105-12-411 |
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author | Knijnenburg, Theo A Lin, Jake Rovira, Hector Boyle, John Shmulevich, Ilya |
author_facet | Knijnenburg, Theo A Lin, Jake Rovira, Hector Boyle, John Shmulevich, Ilya |
author_sort | Knijnenburg, Theo A |
collection | PubMed |
description | BACKGROUND: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1]. RESULTS: The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded. CONCLUSIONS: Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way. AVAILABILITY: http://informatics.systemsbiology.net/EPEPT/ |
format | Online Article Text |
id | pubmed-3277916 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-32779162012-02-13 EPEPT: A web service for enhanced P-value estimation in permutation tests Knijnenburg, Theo A Lin, Jake Rovira, Hector Boyle, John Shmulevich, Ilya BMC Bioinformatics Software BACKGROUND: In computational biology, permutation tests have become a widely used tool to assess the statistical significance of an event under investigation. However, the common way of computing the P-value, which expresses the statistical significance, requires a very large number of permutations when small (and thus interesting) P-values are to be accurately estimated. This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values [1]. RESULTS: The proposed P-value estimator has been enriched with additional functionalities and is made available to the general community through a public website and web service, called EPEPT. This means that the EPEPT routines can be accessed not only via a website, but also programmatically using any programming language that can interact with the web. Examples of web service clients in multiple programming languages can be downloaded. Additionally, EPEPT accepts data of various common experiment types used in computational biology. For these experiment types EPEPT first computes the permutation values and then performs the P-value estimation. Finally, the source code of EPEPT can be downloaded. CONCLUSIONS: Different types of users, such as biologists, bioinformaticians and software engineers, can use the method in an appropriate and simple way. AVAILABILITY: http://informatics.systemsbiology.net/EPEPT/ BioMed Central 2011-10-24 /pmc/articles/PMC3277916/ /pubmed/22024252 http://dx.doi.org/10.1186/1471-2105-12-411 Text en Copyright © 2011 Knijnenburg et al; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Knijnenburg, Theo A Lin, Jake Rovira, Hector Boyle, John Shmulevich, Ilya EPEPT: A web service for enhanced P-value estimation in permutation tests |
title | EPEPT: A web service for enhanced P-value estimation in permutation tests |
title_full | EPEPT: A web service for enhanced P-value estimation in permutation tests |
title_fullStr | EPEPT: A web service for enhanced P-value estimation in permutation tests |
title_full_unstemmed | EPEPT: A web service for enhanced P-value estimation in permutation tests |
title_short | EPEPT: A web service for enhanced P-value estimation in permutation tests |
title_sort | epept: a web service for enhanced p-value estimation in permutation tests |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277916/ https://www.ncbi.nlm.nih.gov/pubmed/22024252 http://dx.doi.org/10.1186/1471-2105-12-411 |
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