MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Release (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 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 1.6.0
In Bioconductor since BioC 3.4 (R-3.3) (1.5 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
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
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 http://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report Download Stats

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