MultiAssayExperiment
Software for the integration of multi-omics experiments in Bioconductor
Bioconductor version: 3.23 · Package version: 1.38.0
Harmonize 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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MultiAssayExperiment")Details
| Maintainer | Marcel Ramos <marcel.ramos@sph.cuny.edu> |
| Author | Marcel Ramos [aut, cre] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Martin Morgan [aut, ctb], Lori Shepherd [ctb], Hervé Pagès [ctb], Vincent J Carey [aut, ctb], Levi Waldron [aut], MultiAssay SIG [ctb], NCI [fnd] (GrantNo.: U24CA289073) |
| License | Artistic-2.0 |
| URL | http://waldronlab.io/MultiAssayExperiment/ |
| Bug Reports | https://github.com/waldronlab/MultiAssayExperiment/issues |
| Downloads rank | 8577 |
| Source branch | RELEASE_3_23 |
| biocViews | DataRepresentation, Infrastructure, Software |
Documentation
- MultiAssayExperiment: The Integrative Bioconductor Container
- Using DelayedMatrix with MultiAssayExperiment
- MultiAssayExperiment Cheatsheet
- MultiAssayExperiment: Quick Start Guide
Download
Dependencies
Depends: SummarizedExperiment, R (>= 4.5.0)
Imports: Biobase, BiocBaseUtils, BiocGenerics, DelayedArray, GenomicRanges, IRanges, MatrixGenerics, methods, S4Vectors, tidyr, utils
Suggests: BiocStyle, HDF5Array, h5mread, knitr, maftools, RaggedExperiment, reshape2, rmarkdown, survival, survminer, testthat, UpSetR
Reverse dependencies
Depends On Me (23): alabaster.mae, CAGEr, cBioPortalData, ClassifyR, curatedPCaData, curatedTCGAData, evaluomeR, hipathia, HoloFoodR, InTAD, MGnifyR, mia, microbiomeDataSets, midasHLA, MIRit, missRows, OMICsPCAdata, QFeatures, RFLOMICS, scMultiome, SingleCellMultiModal, terraTCGAdata, tidyexposomics
Imports Me (50): AffiXcan, AMARETTO, anansi, animalcules, autonomics, biosigner, caretMultimodal, CoreGx, corral, curatedTBData, ELMER, FindIT2, gDRcore, gDRimport, gDRutils, gINTomics, glmSparseNet, GOpro, hermes, HMP2Data, LegATo, Lheuristic, LinkHD, metabolomicsWorkbenchR, MetaScope, MOMA, MOSClip, msqrob2, MuData, MultiBaC, MultimodalExperiment, nipalsMCIA, OMICsPCA, omicsPrint, omXplore, padma, PDATK, PharmacoGx, phenomis, ropls, scGraphVerse, scp, scPipe, SmartPhos, survClust, TCGAutils, TENET, TENET.ExperimentHub, vsclust, xcore
Suggests Me (14): BatchQC, BiocGenerics, brgedata, CNVRanger, funOmics, maftools, MOFA2, MOFAdata, MultiDataSet, R.ComDim, RaggedExperiment, teal, teal.slice, updateObject