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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

Graphical representation of a typical Mixed Model data structure.The Mixed Model analysis requires a data structure where there are multiple batches of knockout animals and regular batches of control animals. The analysis does not require concurrent controls.
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pone.0131274.g003: Graphical representation of a typical Mixed Model data structure.The Mixed Model analysis requires a data structure where there are multiple batches of knockout animals and regular batches of control animals. The analysis does not require concurrent controls.

Mentions: This framework can be used in cases where both controls and treatment (e.g. knockout mice) are measured over multiple batches. The treatment animals do not have to be concurrent with controls (Fig 3).


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)

Graphical representation of a typical Mixed Model data structure.The Mixed Model analysis requires a data structure where there are multiple batches of knockout animals and regular batches of control animals. The analysis does not require concurrent controls.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131274.g003: Graphical representation of a typical Mixed Model data structure.The Mixed Model analysis requires a data structure where there are multiple batches of knockout animals and regular batches of control animals. The analysis does not require concurrent controls.
Mentions: This framework can be used in cases where both controls and treatment (e.g. knockout mice) are measured over multiple batches. The treatment animals do not have to be concurrent with controls (Fig 3).

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