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MultiAssayExperiment

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

All versions 3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Software for the integration of multi-omics experiments in Bioconductor


Bioconductor version: Development (3.24)

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 iD 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], NCI [fnd] (GrantNo.: U24CA289073)

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

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

Marcel Ramos, Martin Morgan, Vincent J Carey, Levi Waldron. MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor. doi:10.18129/B9.bioc.MultiAssayExperiment, R package version 1.39.1, https://bioconductor.org/packages/MultiAssayExperiment.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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")
MultiAssayExperiment Cheatsheet HTML
Coordinating Analysis of Multi-Assay Experiments HTML R Script
Quick-start Guide HTML R Script
HDF5Array and MultiAssayExperiment HTML R Script
Reference ManualPDF
NEWSText
VideoVideo
VideoVideo
Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software
Version1.39.1
In Bioconductor sinceBioC 3.4 (R-3.3) (10 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
URLhttp://waldronlab.io/MultiAssayExperiment/
Bug Reportshttps://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, curatedPCaData, curatedTCGAData, evaluomeR, hipathia, HoloFoodR, InTAD, MGnifyR, mia, microbiomeDataSets, midasHLA, MIRit, missRows, MultiAssaySpatialExperiment, OMICsPCAdata, QFeatures, RFLOMICS, scMultiome, SingleCellMultiModal, terraTCGAdata, tidyexposomics
Imports Me AffiXcan, AMARETTO, anansi, animalcules, autonomics, BiocDuckDB, biosigner, caretMultimodal, CoreGx, CorNetto, corral, curatedTBData, DAssemble, ELMER, FindIT2, gDR, gDRcore, gDRimport, gDRutils, gINTomics, glmSparseNet, GOpro, GPlinksR, hermes, HuMMANet, LegATo, Lheuristic, LinkHD, metabolomicsWorkbenchR, MetaScope, MOMA, MOSClip, msqrob2, MuData, MultiBaC, MultimodalExperiment, MultiOmicsBridge, nipalsMCIA, OMICsPCA, omicsPrint, omXplore, padma, PDATK, PharmacoGx, phenomis, QFeaturesGUI, ropls, scGraphVerse, scp, scPipe, SmartPhos, survClust, TCGAutils, TENET, TENET.ExperimentHub, vsclust, xcore
Suggests Me BatchQC, BiocGenerics, brgedata, CNVRanger, DaparToolshed, funOmics, maftools, MOFA2, MOFAdata, MultiDataSet, OmicsBraid, R.ComDim, RaggedExperiment, S4Cartographer, TDbasedUFEadv, teal, teal.slice, updateObject
Links To Me
Build Report Build Report, r-universe

Package Archives

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

Source Package MultiAssayExperiment_1.39.1.tar.gz
Windows Binary (x86_64) MultiAssayExperiment_1.39.1.zip
macOS Binary (big-sur-x86_64) MultiAssayExperiment_1.39.1.tgz
macOS Binary (sonoma-arm64) MultiAssayExperiment_1.39.1.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/MultiAssayExperiment
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/MultiAssayExperiment
Package Short Url https://bioconductor.org/packages/MultiAssayExperiment/
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