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>
LicenseLGPL
Version1.16.0
http://www.isa-tools.org/

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

Functions

[<-,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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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