MultiAssayExperiment

DOI: 10.18129/B9.bioc.MultiAssayExperiment    

This is the development version of MultiAssayExperiment; for the stable release version, see MultiAssayExperiment.

Software for the integration of multi-omics experiments in Bioconductor

Bioconductor version: Development (3.8)

MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.

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")

 

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 1.7.9
In Bioconductor since BioC 3.4 (R-3.3) (1.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), SummarizedExperiment(>= 1.3.81)
Imports methods, GenomicRanges(>= 1.25.93), BiocGenerics, 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 ELMER, GOpro, omicsPrint, TCGAutils
Suggests Me BiocOncoTK, brgedata, RaggedExperiment
Build Report  

Package Archives

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

Source Package MultiAssayExperiment_1.7.9.tar.gz
Windows Binary MultiAssayExperiment_1.7.9.zip
Mac OS X 10.11 (El Capitan) MultiAssayExperiment_1.7.9.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 http://bioconductor.org/packages/MultiAssayExperiment/
Package Downloads Report Download Stats

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