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Risa is an R package that is part of the ISA tools suite (http://isa-tools.org). Risa supports parsing, saving and updating ISA-tab datasets. It also builds bridges from the ISA-Tab syntax to analysis pipelines for specific assay types, such as mass spectrometry and DNA microarray assays, by building R objects from the metadata required for other packages downstream, such as xcms and affy, respectively. In addition, Risa includes functionality to suggest packages in BioConductor that might be relevant for the assay types in the ISA-TAB dataset being considered. This recommentation functionality relies on the BioCViews annotations provided by each BioConductor package.

The Risa package is available in Bioconductor:

For more information about the ISA tools, consider:

Read the Paper in BMC Bioinformatics!

Access the Open Access BMC Bioinformatics article on Risa here.

Alejandra González-Beltrán, Steffen Neumann, Eamonn Maguire, Susanna-Assunta Sansone and Philippe Rocca-Serra.
The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again BMC Bioinformatics 2014, 15(Suppl 1):S11 doi:10.1186/1471-2105-15-S1-S11

Development

If you have feature requests or find any issues when using Risa, please let us know through the issues tracker at [https://github.com/ISA-tools/Risa/issues].

Contributing

You should read this article about Git Flow: http://scottchacon.com/2011/08/31/github-flow.html. It's a really useful tutorial on how to use Git for collaborative development.

  1. Fork it.
  2. Clone your forked repository to your machine
  3. Create a branch (git checkout -b myRisa)
  4. Make your changes
  5. Run the tests (mvn clean test)
  6. Commit your changes (git commit -am "Added something useful")
  7. Push to the branch (git push origin myRisa)
  8. Create a Pull Request from your branch.
  9. Promote it. Get others to drop in and +1 it.

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Version

Version

1.14.0

License

LGPL

Maintainer

Alejandra GonzalezBeltran

Last Published

February 15th, 2017

Functions in Risa (1.14.0)

getExpressionSet

Retrieves an ExpressionSet for a DNA microarray assay.
isMicroarrayAssay

Determines if an assay is microarray-based or not.
AssayTab-class

Class "AssayTab", a class for maintaing the information of AssayTab
write.assay.file

Write an Assay File from the ISA-Tab dataset
getStudyFilename

Retrieves the study filename to which an assay.filename corresponds.
readISAtab

Reads an ISAtab dataset into an R object.
suggestBiocPackage

Suggest Bioconductor pacakges
getAnnotatedDataFrameAssay

Retrieves an AnnotatedDataFrameAssay.
processAssayXcmsSet.1factor

Build an xcmsSet object given a mass spectrometry assay and considering the first factor defined
processAssayXcmsSet

Build an xcmsSet object given a mass spectrometry assay and considering all factors defined
getMSAssayFilenames

Retrieves a vector with the assay filenames corresponding to mass spectrometry.
isMSAssay

Indicates if an assay filename corresponds to a mass spectrometry assay.
getMIAMEMetadata

Retrieves the MIAME information about a microarray experiment
write.investigation.file

Writes the Investigation File of an ISA-Tab dataset
ISATab-class

Class "ISATab", a class for maintaing ISATab information
getRawDataFilenames-methods

~~ Methods for Function getRawDataFilenames in Package Risa ~~
Risa

Risa package overview
updateAssayMetadata

Update metadata into the assay file
getMicroarrayAssayFilenames

Listing filenames of microarray-based asssay from an ISAtab dataset.
write.ISAtab

Write an ISA-Tab dataset
getAssayRawDataFilenames-methods

~~ Methods for Function getAssayRawDataFilenames in Package Risa ~~
write.study.file

Write a Study File of an ISA-Tab dataset