MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

Software for the Integration of Multi-omics Experiments in Bioconductor

Bioconductor version: Release (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>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("MultiAssayExperiment")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MultiAssayExperiment")

 

PDF		MultiAssayExperiment_cheatsheet.pdf
HTML	R Script	Coordinating Analysis of Multi-Assay Experiments
HTML	R Script	HDF5Array and MultiAssayExperiment
HTML	R Script	Quick-start Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.4.9
In Bioconductor since	BioC 3.4 (R-3.3) (1.5 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
LinkingTo
Suggests	BiocStyle, testthat, knitr, R.rsp, GenomicFiles, HDF5Array, RaggedExperiment, rmarkdown, UpSetR, survival, survminer
SystemRequirements
Enhances
URL	https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API
BugReports	https://github.com/waldronlab/MultiAssayExperiment/issues
Depends On Me	curatedTCGAData, yriMulti
Imports Me	ELMER, GOpro
Suggests Me	brgedata, MultiDataSet, RaggedExperiment, RTCGAToolbox
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
Package Short Url	http://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive