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Bioconductor - MultiAssayExperiment (development version)

MultiAssayExperiment

This is the development version of MultiAssayExperiment; for the stable release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Development (3.22)

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.

Author: Marcel Ramos [aut, cre] ORCID: 0000-0002-3242-0582 , Martin Morgan [aut, ctb], Lori Shepherd [ctb], Hervé Pagès [ctb], Vincent J Carey [aut, ctb], Levi Waldron [aut], MultiAssay SIG [ctb]

Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>

Citation (from within R, enter citation("MultiAssayExperiment")): Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("MultiAssayExperiment")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MultiAssayExperiment")
Details biocViews DataRepresentation, Infrastructure, Software Version 1.35.3 In Bioconductor since BioC 3.4 (R-3.3) (8.5 years) License Artistic-2.0 Depends SummarizedExperiment, R (>= 4.5.0) Imports Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors, tidyr, utils System Requirements URL http://waldronlab.io/MultiAssayExperiment/ Bug Reports https://github.com/waldronlab/MultiAssayExperiment/issues See More Suggests BiocStyle, HDF5Array, h5mread, knitr, maftools, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR Linking To Enhances Depends On Me alabaster.mae, CAGEr, cBioPortalData, ClassifyR, evaluomeR, hipathia, HoloFoodR, InTAD, MGnifyR, mia, midasHLA, MIRit, missRows, QFeatures, RFLOMICS, terraTCGAdata, curatedPCaData, curatedTCGAData, microbiomeDataSets, OMICsPCAdata, scMultiome, SingleCellMultiModal Imports Me AffiXcan, AMARETTO, animalcules, autonomics, biosigner, CoreGx, corral, ELMER, FindIT2, gDRcore, gDRimport, gDRutils, gINTomics, glmSparseNet, GOpro, hermes, Lheuristic, LinkHD, metabolomicsWorkbenchR, MOMA, MOSClip, msqrob2, MuData, MultiBaC, MultimodalExperiment, nipalsMCIA, OMICsPCA, omicsPrint, omXplore, padma, PDATK, PharmacoGx, phenomis, ropls, scp, scPipe, survClust, TCGAutils, TENET, vsclust, xcore, curatedTBData, HMP2Data, LegATo, MetaScope, TENET.ExperimentHub Suggests Me BiocGenerics, CNVRanger, funOmics, maftools, MOFA2, MultiDataSet, RaggedExperiment, updateObject, brgedata, MOFAdata, teal, teal.slice Links To Me Build Report Build Report Package Archives

Follow Installation instructions to use this package in your R session.

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