MultiAssayExperiment
Software for the integration of multi-omics experiments in Bioconductor
Bioconductor version: Release (3.17)
MultiAssayExperiment harmonizes data management of multiple experimental 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. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.
Author: Marcel Ramos [aut, cre] 
, Levi Waldron [aut], MultiAssay SIG [ctb]
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
citation("MultiAssayExperiment")):
Installation
To install this package, start R (version "4.3") 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 | ||
| Quick-start Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| MultiAssayExperiment demo | Video | |
| Marcel Ramos, Workshop 200: MultiAssayExperiment and curatedTCGAData Bioconductor 2020 workshop | Video |
Details
| biocViews | DataRepresentation, Infrastructure, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0), SummarizedExperiment(>= 1.3.81) |
| Imports | methods, GenomicRanges(>= 1.25.93), BiocBaseUtils, BiocGenerics, DelayedArray, S4Vectors(>= 0.23.19), IRanges, Biobase, stats, tidyr, utils |
| Linking To | |
| Suggests | BiocStyle, HDF5Array(>= 1.19.17), knitr, maftools(>= 2.7.10), rmarkdown, R.rsp, RaggedExperiment, UpSetR, survival, survminer, testthat |
| System Requirements | |
| Enhances | |
| URL | http://waldronlab.io/MultiAssayExperiment/ |
| Bug Reports | https://github.com/waldronlab/MultiAssayExperiment/issues |
See More
| Depends On Me | alabaster.mae, CAGEr, cBioPortalData, ClassifyR, curatedTCGAData, evaluomeR, glmSparseNet, hipathia, InTAD, mia, microbiomeDataSets, midasHLA, missRows, OMICsPCAdata, QFeatures, scMultiome, SingleCellMultiModal, terraTCGAdata, TimiRGeN |
| Imports Me | AffiXcan, AMARETTO, animalcules, autonomics, biosigner, CoreGx, corral, curatedTBData, ELMER, FindIT2, FLAMES, GOpro, hermes, HMP2Data, LinkHD, metabolomicsWorkbenchR, MetaScope, MOMA, msqrob2, MuData, MultiBaC, MultimodalExperiment, netDx, OMICsPCA, omicsPrint, padma, PDATK, PharmacoGx, phenomis, ropls, scp, scPipe, TCGAutils, TCGAWorkflow, vsclust, xcore |
| Suggests Me | BiocOncoTK, brgedata, CNVRanger, deco, maftools, MOFA2, MOFAdata, MultiDataSet, RaggedExperiment, updateObject |
| Links To Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MultiAssayExperiment_1.26.0.tar.gz |
| Windows Binary | MultiAssayExperiment_1.26.0.zip |
| macOS Binary (x86_64) | MultiAssayExperiment_1.26.0.tgz |
| macOS Binary (arm64) | MultiAssayExperiment_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MultiAssayExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MultiAssayExperiment |
| Bioc Package Browser | https://code.bioconductor.org/browse/MultiAssayExperiment/ |
| Package Short Url | https://bioconductor.org/packages/MultiAssayExperiment/ |
| Package Downloads Report | Download Stats |