MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Release (3.14)

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	Coordinating Analysis of Multi-Assay Experiments
HTML	R Script	HDF5Array and MultiAssayExperiment
PDF		MultiAssayExperiment_cheatsheet.pdf
HTML	R Script	Quick-start Guide
PDF		Reference Manual
Text		NEWS
Video		MultiAssayExperiment demo
Video		Marcel Ramos, Workshop 200: MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.20.0
In Bioconductor since	BioC 3.4 (R-3.3) (5.5 years)
License	Artistic-2.0
Depends	R (>= 4.0.0), SummarizedExperiment(>= 1.3.81)
Imports	methods, GenomicRanges(>= 1.25.93), BiocGenerics, S4Vectors(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils
LinkingTo
Suggests	BiocStyle, HDF5Array(>= 1.19.17), knitr, maftools(>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat
SystemRequirements
Enhances
URL	http://waldronlab.io/MultiAssayExperiment/
BugReports	https://github.com/waldronlab/MultiAssayExperiment/issues
Depends On Me	CAGEr, cBioPortalData, ClassifyR, curatedTCGAData, evaluomeR, glmSparseNet, hipathia, InTAD, mia, microbiomeDataSets, midasHLA, missRows, OMICsPCAdata, QFeatures, SingleCellMultiModal, TimiRGeN
Imports Me	AffiXcan, AMARETTO, animalcules, autonomics, ClassifyR, CoreGx, corral, curatedTBData, ELMER, FindIT2, GOpro, HMP2Data, LinkHD, metabolomicsWorkbenchR, MOMA, MultiBaC, netDx, OMICsPCA, omicsPrint, padma, PDATK, PharmacoGx, scp, TCGAutils
Suggests Me	BiocOncoTK, brgedata, CNVRanger, deco, maftools, MOFA2, MOFAdata, MultiDataSet, RaggedExperiment
Links To Me
Build Report

Package Archives

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

Source Package	MultiAssayExperiment_1.20.0.tar.gz
Windows Binary	MultiAssayExperiment_1.20.0.zip
macOS 10.13 (High Sierra)	MultiAssayExperiment_1.20.0.tgz
Source Repository	git 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/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.14	Source Archive