MultiAssayExperiment

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

DOI: 10.18129/B9.bioc.MultiAssayExperiment

Bioconductor version: 3.18

MultiAssayExperiment harmonizes 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] , Levi Waldron [aut], MultiAssay SIG [ctb]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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

Installation

To install this package, start R (version "4.3") and enter:


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

Coordinating Analysis of Multi-Assay Experiments HTML R Script

HDF5Array and MultiAssayExperiment HTML R Script

MultiAssayExperiment_cheatsheet.pdf PDF

Quick-start Guide HTML R Script

Reference Manual PDF

NEWS Text

MultiAssayExperiment demo Video

Marcel Ramos, Workshop 200: MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop Video

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataRepresentation, Infrastructure, Software

Version 1.28.0

In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)

License Artistic-2.0

Depends R (>= 4.2.0), SummarizedExperiment(>= 1.3.81)

Imports methods, GenomicRanges(>= 1.25.93), BiocBaseUtils, BiocGenerics, DelayedArray, S4Vectors(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils

System Requirements

URL http://waldronlab.io/MultiAssayExperiment/

Bug Reports https://github.com/waldronlab/MultiAssayExperiment/issues

Suggests BiocStyle, HDF5Array(>= 1.19.17), knitr, maftools(>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat

Linking To

Enhances

Depends On Me alabaster.mae, CAGEr, cBioPortalData, ClassifyR, curatedTCGAData, evaluomeR, glmSparseNet, hipathia, InTAD, mia, microbiomeDataSets, midasHLA, missRows, OMICsPCAdata, QFeatures, scMultiome, SingleCellMultiModal, terraTCGAdata, TimiRGeN

Imports Me AffiXcan, AMARETTO, animalcules, autonomics, biosigner, CoreGx, corral, curatedTBData, ELMER, FindIT2, FLAMES, gDRcore, gDRimport, gDRutils, GOpro, hermes, HMP2Data, LinkHD, metabolomicsWorkbenchR, MetaScope, MOMA, msqrob2, MuData, MultiBaC, MultimodalExperiment, netDx, nipalsMCIA, OMICsPCA, omicsPrint, padma, PDATK, PharmacoGx, phenomis, ropls, scp, scPipe, TCGAutils, TCGAWorkflow, vsclust, xcore

Suggests Me BiocOncoTK, brgedata, CNVRanger, deco, maftools, MOFA2, MOFAdata, MultiDataSet, RaggedExperiment, updateObject

Links To Me

Build Report Build Report

Package Archives

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

Source Package MultiAssayExperiment_1.28.0.tar.gz

Windows Binary MultiAssayExperiment_1.28.0.zip

macOS Binary (x86_64) MultiAssayExperiment_1.28.0.tgz

macOS Binary (arm64) MultiAssayExperiment_1.28.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/MultiAssayExperiment

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/MultiAssayExperiment

Bioc Package Browser https://code.bioconductor.org/browse/MultiAssayExperiment/

Package Short Url https://bioconductor.org/packages/MultiAssayExperiment/

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