MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Release (3.13)

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 "4.1") and enter:

if (!requireNamespace("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 1.18.0
In Bioconductor since BioC 3.4 (R-3.3) (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, microbiomeDataSets, midasHLA, missRows, OMICsPCAdata, QFeatures, SingleCellMultiModal, TimiRGeN
Imports Me AffiXcan, AMARETTO, animalcules, autonomics, CoreGx, corral, ELMER, 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_1.18.0.tar.gz
Windows Binary MultiAssayExperiment_1.18.0.zip
macOS 10.13 (High Sierra) MultiAssayExperiment_1.18.0.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

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