MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: 3.7

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.

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")

 

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

Details

biocViews	DataRepresentation, Infrastructure, Software
Version	1.6.0
In Bioconductor since	BioC 3.4 (R-3.3) (2 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	methods, GenomicRanges(>= 1.25.93), BiocGenerics, SummarizedExperiment(>= 1.3.81), S4Vectors(>= 0.17.5), IRanges, Biobase, stats, tidyr, utils
LinkingTo
Suggests	BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer
SystemRequirements
Enhances
URL	https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API
BugReports	https://github.com/waldronlab/MultiAssayExperiment/issues
Depends On Me	ClassifyR, curatedTCGAData, hipathia, InTAD, missRows, yriMulti
Imports Me	CAGEr, ELMER, GOpro, omicsPrint, TCGAutils
Suggests Me	BiocOncoTK, brgedata, MultiDataSet, RaggedExperiment
Links To Me
Build Report

Package Archives

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

Source Package	MultiAssayExperiment_1.6.0.tar.gz
Windows Binary	MultiAssayExperiment_1.6.0.zip
Mac OS X 10.11 (El Capitan)	MultiAssayExperiment_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MultiAssayExperiment
Source Repository (Developer Access)	git clone [email protected]:packages/MultiAssayExperiment
Package Short Url	http://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report	Download Stats