Dataset Information

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

ABSTRACT:

Motivation

The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data.

Results

We have updated maSigPro to support RNA-seq time series analysis by introducing generalized linear models in the algorithm to support the modeling of count data while maintaining the traditional functionalities of the package. We show a good performance of the maSigPro-GLM method in several simulated time-course scenarios and in a real experimental dataset.

Availability and implementation

The package is freely available under the LGPL license from the Bioconductor Web site (http://bioconductor.org).

SUBMITTER: Nueda MJ

PROVIDER: S-EPMC4155246 | biostudies-literature | 2014 Sep

REPOSITORIES: biostudies-literature

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Publications

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Nueda María José MJ Tarazona Sonia S Conesa Ana A

Bioinformatics (Oxford, England) 20140603 18

<h4>Motivation</h4>The widespread adoption of RNA-seq to quantitatively measure gene expression has increased the scope of sequencing experimental designs to include time-course experiments. maSigPro is an R package specifically suited for the analysis of time-course gene expression data, which was developed originally for microarrays and hence was limited in its application to count data.<h4>Results</h4>We have updated maSigPro to support RNA-seq time series analysis by introducing generalized ...[more]

PMID: 24894503

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Project description:BackgroundThe interpretation of results from transcriptome profiling experiments via RNA sequencing (RNA-seq) can be a complex task, where the essential information is distributed among different tabular and list formats-normalized expression values, results from differential expression analysis, and results from functional enrichment analyses. A number of tools and databases are widely used for the purpose of identification of relevant functional patterns, yet often their contextualization within the data and results at hand is not straightforward, especially if these analytic components are not combined together efficiently.ResultsWe developed the GeneTonic software package, which serves as a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses, by fully leveraging the information of expression values in a differential expression context. GeneTonic is implemented in R and Shiny, leveraging packages that enable HTML-based interactive visualizations for executing drilldown tasks seamlessly, viewing the data at a level of increased detail. GeneTonic is integrated with the core classes of existing Bioconductor workflows, and can accept the output of many widely used tools for pathway analysis, making this approach applicable to a wide range of use cases. Users can effectively navigate interlinked components (otherwise available as flat text or spreadsheet tables), bookmark features of interest during the exploration sessions, and obtain at the end a tailored HTML report, thus combining the benefits of both interactivity and reproducibility.ConclusionGeneTonic is distributed as an R package in the Bioconductor project ( https://bioconductor.org/packages/GeneTonic/ ) under the MIT license. Offering both bird's-eye views of the components of transcriptome data analysis and the detailed inspection of single genes, individual signatures, and their relationships, GeneTonic aims at simplifying the process of interpretation of complex and compelling RNA-seq datasets for many researchers with different expertise profiles.

Dataset Information

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Motivation

Results

Availability and implementation

Publications

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series.

Similar Datasets

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