MultiAssayExperiment

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see MultiAssayExperiment.

Software for the Integration of Multi-omics Experiments in Bioconductor

Bioconductor version: 3.6

Multi-assay 'omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment or ExpressionSet.

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 "3.4") 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")

MultiAssayExperiment_cheatsheet.pdf	PDF
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.4.9
In Bioconductor since	BioC 3.4 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0)
Imports	methods, GenomicRanges(>= 1.25.93), BiocGenerics, SummarizedExperiment(>= 1.3.81), S4Vectors, IRanges, Biobase, reshape2, shinydashboard, shiny, stats, tidyr, utils
System Requirements
URL	https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API
Bug Reports	https://github.com/waldronlab/MultiAssayExperiment/issues

Suggests	BiocStyle, testthat, knitr, R.rsp, GenomicFiles, HDF5Array, RaggedExperiment, rmarkdown, UpSetR, survival, survminer
Linking To
Enhances
Depends On Me	curatedTCGAData, yriMulti
Imports Me	ELMER, GOpro
Suggests Me	brgedata, MultiDataSet, RaggedExperiment, RTCGAToolbox
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	MultiAssayExperiment_1.4.9.tar.gz
Windows Binary	MultiAssayExperiment_1.4.9.zip
Mac OS X 10.11 (El Capitan)	MultiAssayExperiment_1.4.9.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 3.6	Source Archive