Package: MultiAssayExperiment 1.31.3

Marcel Ramos

MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Authors:Marcel Ramos [aut, cre], Martin Morgan [aut, ctb], Lori Shepherd [ctb], Hervé Pagès [ctb], Vincent J Carey [aut, ctb], Levi Waldron [aut], MultiAssay SIG [ctb]

MultiAssayExperiment_1.31.3.tar.gz
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MultiAssayExperiment.pdf |MultiAssayExperiment.html✨
MultiAssayExperiment/json (API)
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Bug tracker:https://github.com/waldronlab/multiassayexperiment/issues

On BioConductor:MultiAssayExperiment-1.31.3(bioc 3.20)MultiAssayExperiment-1.30.2(bioc 3.19)

bioconductor-package

52 exports 7.02 score 49 dependencies 124 dependents 16 mentions

Last updated 1 months agofrom:66eed8e03c

Exports:anyReplicatedassayassayscoercecolDatacolData<-colnamescolnames<-complete.casesDataFramedropsdrops<-ExperimentListexperimentsexperiments<-exportClassgetWithColDatahasAssayhasRowRangesintersectColumnsintersectRowsisEmptylistToMaploadHDF5MultiAssayExperimentlongFormatmakeHitListmapToListMatchedAssayExperimentmergeReplicatesmetadatametadata<-MultiAssayExperimentMultiAssayExperimentToMAFprepMultiAssayrenameColnamerenamePrimaryreplicatedreplicatesrownamessampleMapsampleMap<-saveHDF5MultiAssayExperimentshowshowReplicatedsplitAssayssubsetByAssaysubsetByColDatasubsetByColumnsubsetByRowupdateObjectupsetSampleswideFormat

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicpp11crayoncurlDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc