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

Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA - PLoS ONE (2015)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
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.

No MeSH data available.


The PhenStat package's three-layer structure.The PhenStat package is designed with a three layer structure: dataset processing, analysis and result. In addition, there is a layer with graphical output.
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pone.0131274.g001: The PhenStat package's three-layer structure.The PhenStat package is designed with a three layer structure: dataset processing, analysis and result. In addition, there is a layer with graphical output.

Mentions: For ease of use, the package consists of three layers as shown in Fig 1.


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

Kurbatova N, Mason JC, Morgan H, Meehan TF, Karp NA - PLoS ONE (2015)

The PhenStat package's three-layer structure.The PhenStat package is designed with a three layer structure: dataset processing, analysis and result. In addition, there is a layer with graphical output.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493137&req=5

pone.0131274.g001: The PhenStat package's three-layer structure.The PhenStat package is designed with a three layer structure: dataset processing, analysis and result. In addition, there is a layer with graphical output.
Mentions: For ease of use, the package consists of three layers as shown in Fig 1.

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: The EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

ABSTRACT
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.

No MeSH data available.