Package: Risa 1.47.0

Alejandra Gonzalez-Beltran

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.

Authors:Alejandra Gonzalez-Beltran, Audrey Kauffmann, Steffen Neumann, Gabriella Rustici, ISA Team

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Risa.pdf |Risa.html✨
Risa/json (API)
NEWS

# Install 'Risa' in R:
install.packages('Risa', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/isa-tools/risa/issues

On BioConductor:Risa-1.47.0(bioc 3.20)Risa-1.46.0(bioc 3.19)

bioconductor-package

19 exports 1.38 score 143 dependencies 2 mentions

Last updated 2 months agofrom:8cc4b0e7fd

Exports:getAnnotatedDataFrameAssaygetAssayRawDataFilenamesgetExpressionSetgetMIAMEMetadatagetMicroarrayAssayFilenamesgetMSAssayFilenamesgetRawDataFilenamesgetStudyFilenameisMicroarrayAssayisMSAssayprocessAssayXcmsSetprocessAssayXcmsSet.1factorreadISAtabsuggestBiocPackageupdateAssayMetadatawrite.assay.filewrite.investigation.filewrite.ISAtabwrite.study.file

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsBiocManagerBiocParallelbiocViewsbitopsbslibcachemcliclueclustercodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIDelayedArraydigestdoParalleldplyrevaluatefansifarverfastmapfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegraphgtablehighrhmshtmltoolshtmlwidgetshttrigraphimputeIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmamagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmgcvmimeMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmunsellmzIDmzRncdf4nlmeopensslpcaMethodspillarpkgconfigplotlyplyrpreprocessCoreprettyunitsprogresspromisesProtGenericsPSMatchpurrrQFeaturesR6rappdirsRBGLRColorBrewerRcppRCurlreshape2Rhdf5librlangrmarkdownRUnitS4ArraysS4VectorssassscalessnowSparseArraySpectrastatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitevsnwithrxcmsxfunXMLXVectoryamlzlibbioc

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

Rendered fromRisa.Rnwusingutils::Sweaveon Jul 02 2024.

Last update: 2015-03-10
Started: 2013-11-01

Readme and manuals

Help Manual

Help pageTopics
Class '"AssayTab"', a class for maintaing the information of AssayTabAssayTab-class MicroarrayAssayTab-class MSAssayTab-class NMRAssayTab SeqAssayTab [,AssayTab,ANY,ANY,ANY-method [,AssayTab-method [<-,AssayTab,ANY,ANY,ANY-method [<-,AssayTab-method
Retrieves an AnnotatedDataFrameAssay.getAnnotatedDataFrameAssay
~~ Methods for Function 'getAssayRawDataFilenames' in Package 'Risa' ~~getAssayRawDataFilenames getAssayRawDataFilenames,AssayTab,logical-method getAssayRawDataFilenames,MicroarrayAssayTab,logical-method getAssayRawDataFilenames,MSAssayTab,logical-method getAssayRawDataFilenames,NMRAssayTab,logical-method getAssayRawDataFilenames,SeqAssayTab,logical-method getAssayRawDataFilenames-methods
Retrieves an ExpressionSet for a DNA microarray assay.getExpressionSet
Retrieves the MIAME information about a microarray experimentgetMIAMEMetadata
Listing filenames of microarray-based asssay from an ISAtab dataset.getMicroarrayAssayFilenames
Retrieves a vector with the assay filenames corresponding to mass spectrometry.getMSAssayFilenames
~~ Methods for Function 'getRawDataFilenames' in Package 'Risa' ~~getRawDataFilenames getRawDataFilenames,ISATab,logical-method getRawDataFilenames-methods
Retrieves the study filename to which an assay.filename corresponds.getStudyFilename
Class '"ISATab"', a class for maintaing ISATab informationISATab-class [,ISATab,ANY,ANY,ANY-method [,ISATab-method [<-,ISATab,ANY,ANY,ANY-method [<-,ISATab-method
Determines if an assay is microarray-based or not.isMicroarrayAssay
Indicates if an assay filename corresponds to a mass spectrometry assay.isMSAssay
Build an xcmsSet object given a mass spectrometry assay and considering all factors definedprocessAssayXcmsSet
Build an xcmsSet object given a mass spectrometry assay and considering the first factor definedprocessAssayXcmsSet.1factor
Reads an ISAtab dataset into an R object.readISAtab
Risa package overviewRisa-package Risa
Suggest Bioconductor pacakgessuggestBiocPackage
Update metadata into the assay fileupdateAssayMetadata
Write an Assay File from the ISA-Tab datasetwrite.assay.file
Writes the Investigation File of an ISA-Tab datasetwrite.investigation.file
Write an ISA-Tab datasetwrite.ISAtab
Write a Study File of an ISA-Tab datasetwrite.study.file