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>

Citation (from within R, enter citation("MultiAssayExperiment")):

Installation

To install this package, start R (version "3.5") 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")
Coordinating Analysis of Multi-Assay Experiments HTML R Script
HDF5Array and MultiAssayExperiment HTML R Script
MultiAssayExperiment_cheatsheet.pdf PDF
Quick-start Guide HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, Infrastructure, Software
Version 1.6.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 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
System Requirements
URL https://github.com/waldronlab/MultiAssayExperiment/wiki/MultiAssayExperiment-API
Bug Reports https://github.com/waldronlab/MultiAssayExperiment/issues
See More
Suggests BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer
Linking To
Enhances
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 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 git@git.bioconductor.org:packages/MultiAssayExperiment
Package Short Url https://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive