Risa: Converting experimental metadata from ISA-tab into Bioconductor data structures

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The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.

Author
Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team
Date of publication
None
Maintainer
Alejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>
License
LGPL
Version
1.16.0
URLs

View on Bioconductor

Man pages

AssayTab-class
Class '"AssayTab"', a class for maintaing the information of...
getAnnotatedDataFrameAssay
Retrieves an AnnotatedDataFrameAssay.
getAssayRawDataFilenames-methods
~~ Methods for Function 'getAssayRawDataFilenames' in Package...
getExpressionSet
Retrieves an ExpressionSet for a DNA microarray assay.
getMIAMEMetadata
Retrieves the MIAME information about a microarray experiment
getMicroarrayAssayFilenames
Listing filenames of microarray-based asssay from an ISAtab...
getMSAssayFilenames
Retrieves a vector with the assay filenames corresponding to...
getRawDataFilenames-methods
~~ Methods for Function 'getRawDataFilenames' in Package...
getStudyFilename
Retrieves the study filename to which an assay.filename...
ISAtab-class
Class '"ISATab"', a class for maintaing ISATab information
isMicroarrayAssay
Determines if an assay is microarray-based or not.
isMSAssay
Indicates if an assay filename corresponds to a mass...
processAssayXcmsSet
Build an xcmsSet object given a mass spectrometry assay and...
processAssayXcmsSet.1factor
Build an xcmsSet object given a mass spectrometry assay and...
readISAtab
Reads an ISAtab dataset into an R object.
Risa-package
Risa package overview
suggestBiocPackage
Suggest Bioconductor pacakges
updateAssayMetadata
Update metadata into the assay file
write.assay.file
Write an Assay File from the ISA-Tab dataset
write.investigation.file
Writes the Investigation File of an ISA-Tab dataset
write.isatab
Write an ISA-Tab dataset
write.study.file
Write a Study File of an ISA-Tab dataset

Files in this package

Risa/DESCRIPTION
Risa/NAMESPACE
Risa/NEWS
Risa/R
Risa/R/AllClasses.R
Risa/R/AllGenerics.R
Risa/R/Risa-biocViews.R
Risa/R/Risa-microarray.R
Risa/R/Risa-ms.R
Risa/R/Risa.R
Risa/README.md
Risa/TODO
Risa/build
Risa/build/vignette.rds
Risa/inst
Risa/inst/CITATION
Risa/inst/doc
Risa/inst/doc/Risa.R
Risa/inst/doc/Risa.Rnw
Risa/inst/doc/Risa.pdf
Risa/inst/extdata
Risa/inst/extdata/ARMSTRONG-S-3-metadata.zip
Risa/inst/extdata/ISA-BiocViews-mapping.csv
Risa/inst/extdata/faahKO-metadata.zip
Risa/man
Risa/man/AssayTab-class.Rd
Risa/man/ISAtab-class.Rd
Risa/man/Risa-package.Rd
Risa/man/getAnnotatedDataFrameAssay.Rd
Risa/man/getAssayRawDataFilenames-methods.Rd
Risa/man/getExpressionSet.Rd
Risa/man/getMIAMEMetadata.Rd
Risa/man/getMSAssayFilenames.Rd
Risa/man/getMicroarrayAssayFilenames.Rd
Risa/man/getRawDataFilenames-methods.Rd
Risa/man/getStudyFilename.Rd
Risa/man/isMSAssay.Rd
Risa/man/isMicroarrayAssay.Rd
Risa/man/processAssayXcmsSet.1factor.Rd
Risa/man/processAssayXcmsSet.Rd
Risa/man/readISAtab.Rd
Risa/man/suggestBiocPackage.Rd
Risa/man/updateAssayMetadata.Rd
Risa/man/write.assay.file.Rd
Risa/man/write.investigation.file.Rd
Risa/man/write.isatab.Rd
Risa/man/write.study.file.Rd
Risa/vignettes
Risa/vignettes/Risa.Rnw