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

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.

AuthorAlejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team
Date of publicationNone
MaintainerAlejandra Gonzalez-Beltran <alejandra.gonzalez.beltran@gmail.com>

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


[<-,AssayTab,ANY,ANY,ANY-method Man page
[,AssayTab,ANY,ANY,ANY-method Man page
AssayTab-class Man page
[<-,AssayTab-method Man page
[,AssayTab-method Man page
getAnnotatedDataFrameAssay Man page
getAssayRawDataFilenames Man page
getAssayRawDataFilenames,AssayTab,logical-method Man page
getAssayRawDataFilenames-methods Man page
getAssayRawDataFilenames,MicroarrayAssayTab,logical-method Man page
getAssayRawDataFilenames,MSAssayTab,logical-method Man page
getAssayRawDataFilenames,NMRAssayTab,logical-method Man page
getAssayRawDataFilenames,SeqAssayTab,logical-method Man page
getExpressionSet Man page
getMIAMEMetadata Man page
getMicroarrayAssayFilenames Man page
getMSAssayFilenames Man page
getRawDataFilenames Man page
getRawDataFilenames,ISATab,logical-method Man page
getRawDataFilenames-methods Man page
getStudyFilename Man page
[<-,ISATab,ANY,ANY,ANY-method Man page
[,ISATab,ANY,ANY,ANY-method Man page
ISATab-class Man page
[<-,ISATab-method Man page
[,ISATab-method Man page
isMicroarrayAssay Man page
isMSAssay Man page
MicroarrayAssayTab-class Man page
MSAssayTab-class Man page
NMRAssayTab Man page
processAssayXcmsSet Man page
processAssayXcmsSet.1factor Man page
readISAtab Man page
Risa Man page
Risa-package Man page
SeqAssayTab Man page
suggestBiocPackage Man page
updateAssayMetadata Man page
write.assay.file Man page
write.investigation.file Man page
write.ISAtab Man page
write.study.file Man page

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