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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.


Related in: MedlinePlus

Example output of the PhenStat boxplotGenotypeSex function.Shown is the output from the boxplotGenotypeSex function obtained for the ischemic peak contracture pressure from a study on rats comparing SS strain to SS-3BN/Mcwi strain. Graphic highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.
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pone.0131274.g005: Example output of the PhenStat boxplotGenotypeSex function.Shown is the output from the boxplotGenotypeSex function obtained for the ischemic peak contracture pressure from a study on rats comparing SS strain to SS-3BN/Mcwi strain. Graphic highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.

Mentions: The dataset (S1 Dataset) was processed using PhenStat V2.0.1 and the code available in the Supplementary Information (S1 Code). Exploration of raw data (Fig 5 and Fig 6) highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.


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)

Example output of the PhenStat boxplotGenotypeSex function.Shown is the output from the boxplotGenotypeSex function obtained for the ischemic peak contracture pressure from a study on rats comparing SS strain to SS-3BN/Mcwi strain. Graphic highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131274.g005: Example output of the PhenStat boxplotGenotypeSex function.Shown is the output from the boxplotGenotypeSex function obtained for the ischemic peak contracture pressure from a study on rats comparing SS strain to SS-3BN/Mcwi strain. Graphic highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.
Mentions: The dataset (S1 Dataset) was processed using PhenStat V2.0.1 and the code available in the Supplementary Information (S1 Code). Exploration of raw data (Fig 5 and Fig 6) highlights a visual difference in the variable of interest that could potentially be attributed to the genotype change.

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.


Related in: MedlinePlus