Package: MultiAssayExperiment 1.33.1

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_1.33.1.tar.gz
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MultiAssayExperiment.pdf |MultiAssayExperiment.html✨
MultiAssayExperiment/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/waldronlab/multiassayexperiment/issues

Datasets:
  • miniACC - Adrenocortical Carcinoma (ACC) MultiAssayExperiment

On BioConductor:MultiAssayExperiment-1.33.0(bioc 3.21)MultiAssayExperiment-1.32.0(bioc 3.20)

infrastructuredatarepresentationbioconductorbioconductor-packagegenomicsnci-itcrtcga

12.77 score 70 stars 125 packages 654 scripts 52 exports 49 dependencies

Last updated 2 days agofrom:325c85ca26. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 19 2024
R-4.5-winNOTENov 19 2024
R-4.5-linuxNOTENov 19 2024
R-4.4-winNOTENov 19 2024
R-4.4-macNOTENov 19 2024
R-4.3-winNOTENov 19 2024
R-4.3-macNOTENov 19 2024

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

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicpp11crayoncurlDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeopensslpillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc

Cheatsheet for MultiAssayExperiment

Rendered fromMultiAssayExperiment_cheatsheet.pdf.asisusingR.rsp::asison Nov 19 2024.

Last update: 2017-08-18
Started: 2017-08-18

MultiAssayExperiment: The Integrative Bioconductor Container

MultiAssay Special Interest Group

Rendered fromMultiAssayExperiment.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2024-02-02
Started: 2016-03-27

Using DelayedMatrix with MultiAssayExperiment

MultiAssay Special Interest Group

Rendered fromUsingHDF5Array.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2021-10-29
Started: 2016-07-14

MultiAssayExperiment: Quick Start Guide

Marcel Ramos & Levi Waldron

Rendered fromQuickStartMultiAssay.Rmdusingknitr::rmarkdownon Nov 19 2024.

Last update: 2022-05-18
Started: 2017-03-31

Readme and manuals

Help Manual

Help pageTopics
MultiAssayExperiment: Build an integrative multi-assay containerMultiAssayExperiment-package
Represent multiple experiments as a List-derivative 'ExperimentList'ExperimentList
ExperimentList - A container for multi-experiment dataassay,ANY,missing-method assay,ExperimentList,character-method assay,ExperimentList,missing-method assay,ExperimentList,numeric-method assays,ExperimentList-method coerce,List,ExperimentList-method coerce,list,ExperimentList-method coerce-ExperimentList colnames,ExperimentList-method dimnames,ExperimentList-method ExperimentList-class isEmpty,ExperimentList-method mergeReplicates,ExperimentList-method rownames,ExperimentList-method show,ExperimentList-method
Checking assay method for any classhasAssay
Save a MultiAssayExperiment class object to HDF5 and Rds filesHDF5MultiAssayExperiment loadHDF5MultiAssayExperiment saveHDF5MultiAssayExperiment
Convert map from data.frame or DataFrame to list and vice versalistToMap mapToList
MatchedAssayExperiment - A matched-samples MultiAssayExperiment classcoerce,MultiAssayExperiment,MatchedAssayExperiment-method MatchedAssayExperiment MatchedAssayExperiment-class
Adrenocortical Carcinoma (ACC) MultiAssayExperimentminiACC
Construct an integrative representation of multi-omic data with 'MultiAssayExperiment'MultiAssayExperiment
MultiAssayExperiment - An integrative multi-assay class for experiment dataassay,MultiAssayExperiment,character-method assay,MultiAssayExperiment,missing-method assay,MultiAssayExperiment,numeric-method assays,MultiAssayExperiment-method c,MultiAssayExperiment-method coerce,List,MultiAssayExperiment-method coerce,list,MultiAssayExperiment-method coerce-MultiAssayExperiment dimnames,MultiAssayExperiment-method exportClass exportClass,MultiAssayExperiment-method length,MultiAssayExperiment-method MultiAssayExperiment-class names,MultiAssayExperiment-method show,MultiAssayExperiment-method updateObject,MultiAssayExperiment-method
A group of helper functions for manipulating and cleaning a MultiAssayExperimentanyReplicated anyReplicated,MultiAssayExperiment-method complete.cases,MultiAssayExperiment-method getWithColData hasRowRanges hasRowRanges,ExperimentList-method hasRowRanges,MultiAssayExperiment-method intersectColumns intersectRows isEmpty,MultiAssayExperiment-method longFormat makeHitList makeMatchList mergeReplicates mergeReplicates,ANY-method mergeReplicates,MultiAssayExperiment-method MultiAssayExperiment-helpers renameColname renamePrimary replicated replicated,MultiAssayExperiment-method replicates replicates,MultiAssayExperiment-method showReplicated showReplicated,MultiAssayExperiment-method splitAssays splitAssays,MultiAssayExperiment-method wideFormat
Accessing and modifying information in MultiAssayExperiment$,MultiAssayExperiment-method $<-,MultiAssayExperiment-method colData,MultiAssayExperiment-method colData<-,MultiAssayExperiment,ANY-method colData<-,MultiAssayExperiment,DataFrame-method colnames<-,MultiAssayExperiment,List-method colnames<-,MultiAssayExperiment,list-method drops drops,MultiAssayExperiment-method drops<- drops<-,MultiAssayExperiment-method experiments experiments,MultiAssayExperiment-method experiments<- experiments<-,MultiAssayExperiment,ExperimentList-method experiments<-,MultiAssayExperiment,List-method metadata,MultiAssayExperiment-method metadata<-,MultiAssayExperiment-method MultiAssayExperiment-methods names<-,MultiAssayExperiment-method sampleMap sampleMap,MultiAssayExperiment-method sampleMap<- sampleMap<-,MultiAssayExperiment,ANY-method sampleMap<-,MultiAssayExperiment,DataFrame-method
Convert MultiAssayExperiment to MAF classMultiAssayExperimentToMAF
Prepare a 'MultiAssayExperiment' instanceprepMultiAssay
Objects exported from other packagesDataFrame reexports
Subsetting a MultiAssayExperiment objectsubset subsetBy subsetByAssay subsetByAssay,ExperimentList-method subsetByAssay,MultiAssayExperiment-method subsetByColData subsetByColData,MultiAssayExperiment,ANY-method subsetByColData,MultiAssayExperiment,character-method subsetByColumn subsetByColumn,ExperimentList,List-method subsetByColumn,ExperimentList,list-method subsetByColumn,ExperimentList,logical-method subsetByColumn,MultiAssayExperiment,ANY-method subsetByRow subsetByRow,ExperimentList,ANY-method subsetByRow,ExperimentList,List-method subsetByRow,ExperimentList,list-method subsetByRow,ExperimentList,logical-method subsetByRow,MultiAssayExperiment,ANY-method [,MultiAssayExperiment,ANY,ANY,ANY-method [,MultiAssayExperiment,ANY-method [<-,MultiAssayExperiment,ANY,ANY,ANY-method [[,MultiAssayExperiment,ANY,ANY-method [[<-,MultiAssayExperiment,ANY,ANY-method
Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in 'UpSetR'upsetSamples