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PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data

The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here...

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Autores principales: Kurbatova, Natalja, Mason, Jeremy C., Morgan, Hugh, Meehan, Terrence F., Karp, Natasha A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493137/
https://www.ncbi.nlm.nih.gov/pubmed/26147094
http://dx.doi.org/10.1371/journal.pone.0131274
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author Kurbatova, Natalja
Mason, Jeremy C.
Morgan, Hugh
Meehan, Terrence F.
Karp, Natasha A.
author_facet Kurbatova, Natalja
Mason, Jeremy C.
Morgan, Hugh
Meehan, Terrence F.
Karp, Natasha A.
author_sort Kurbatova, Natalja
collection PubMed
description The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here we present PhenStat – a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations. The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation. PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline. The software provides guidance to the user for selecting appropriate analysis methods based on the dataset and is designed to allow for additions and modifications as needed. The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC). By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment.
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spelling pubmed-44931372015-07-15 PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data Kurbatova, Natalja Mason, Jeremy C. Morgan, Hugh Meehan, Terrence F. Karp, Natasha A. PLoS One Research Article The lack of reproducibility with animal phenotyping experiments is a growing concern among the biomedical community. One contributing factor is the inadequate description of statistical analysis methods that prevents researchers from replicating results even when the original data are provided. Here we present PhenStat – a freely available R package that provides a variety of statistical methods for the identification of phenotypic associations. The methods have been developed for high throughput phenotyping pipelines implemented across various experimental designs with an emphasis on managing temporal variation. PhenStat is targeted to two user groups: small-scale users who wish to interact and test data from large resources and large-scale users who require an automated statistical analysis pipeline. The software provides guidance to the user for selecting appropriate analysis methods based on the dataset and is designed to allow for additions and modifications as needed. The package was tested on mouse and rat data and is used by the International Mouse Phenotyping Consortium (IMPC). By providing raw data and the version of PhenStat used, resources like the IMPC give users the ability to replicate and explore results within their own computing environment. Public Library of Science 2015-07-06 /pmc/articles/PMC4493137/ /pubmed/26147094 http://dx.doi.org/10.1371/journal.pone.0131274 Text en © 2015 Kurbatova et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Kurbatova, Natalja
Mason, Jeremy C.
Morgan, Hugh
Meehan, Terrence F.
Karp, Natasha A.
PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title_full PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title_fullStr PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title_full_unstemmed PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title_short PhenStat: A Tool Kit for Standardized Analysis of High Throughput Phenotypic Data
title_sort phenstat: a tool kit for standardized analysis of high throughput phenotypic data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4493137/
https://www.ncbi.nlm.nih.gov/pubmed/26147094
http://dx.doi.org/10.1371/journal.pone.0131274
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