Package: MultimodalExperiment 1.13.0

Lucas Schiffer

MultimodalExperiment: Integrative Bulk and Single-Cell Experiment Container

MultimodalExperiment is an S4 class that integrates bulk and single-cell experiment data; it is optimally storage-efficient, and its methods are exceptionally fast. It effortlessly represents multimodal data of any nature and features normalized experiment, subject, sample, and cell annotations, which are related to underlying biological experiments through maps. Its coordination methods are opt-in and employ database-like join operations internally to deliver fast and flexible management of multimodal data.

Authors:Lucas Schiffer [aut, cre]

MultimodalExperiment_1.13.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MultimodalExperiment/json (API)

# Install 'MultimodalExperiment' in R:

install.packages('MultimodalExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

pbRNAseq - MultimodalExperiment Example Data
scADTseq - MultimodalExperiment Example Data
scRNAseq - MultimodalExperiment Example Data

On BioConductor:MultimodalExperiment-1.13.0(bioc 3.24)MultimodalExperiment-1.12.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

datarepresentation infrastructure singlecell

4.00 score 4 scripts 37 exports 38 dependencies

Last updated from:c54ec6c109. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	176
linux-devel-x86_64	OK	285
source / vignettes	OK	222
linux-release-x86_64	OK	282
macos-release-arm64	OK	211
macos-oldrel-arm64	OK	158
windows-devel	OK	211
windows-release	OK	190
windows-oldrel	OK	191
wasm-release	OK	124

Exports:bulkExperiments bulkExperiments<-cellData cellData<-cellMap cellMap<-colnames colnames<-experiment experiment<-experimentData experimentData<-ExperimentList experimentMap experimentMap<-experimentNames experimentNames<-experiments experiments<-harmonize joinAnnotations joinMaps MultimodalExperiment propagate rownames rownames<-sampleData sampleData<-sampleMap sampleMap<-show singleCellExperiments singleCellExperiments<-subjectData subjectData<-subjectMap subjectMap<-

Dependencies:abind Biobase BiocBaseUtils BiocGenerics cli cpp11 DelayedArray dplyr generics GenomicRanges glue IRanges lattice lifecycle magrittr Matrix MatrixGenerics matrixStats MultiAssayExperiment pillar pkgconfig purrr R6 rlang S4Arrays S4Vectors Seqinfo SparseArray stringi stringr SummarizedExperiment tibble tidyr tidyselect utf8 vctrs withr XVector

MultimodalExperiment

Rendered fromMultimodalExperiment.Rmdusingknitr::rmarkdown

Last update: 2023-04-11
Started: 2023-03-28

Help page	Topics
MultimodalExperiment Annotation Methods	annotation-methods joinAnnotations joinAnnotations,MultimodalExperiment-method
MultimodalExperiment Coordination Methods	coordination-methods harmonize harmonize,MultimodalExperiment-method propagate propagate,MultimodalExperiment-method
MultimodalExperiment Example Data	example-data pbRNAseq scADTseq scRNAseq
MultimodalExperiment Experiment Methods	bulkExperiments bulkExperiments,MultimodalExperiment-method bulkExperiments<- bulkExperiments<-,MultimodalExperiment-method experiment experiment,MultimodalExperiment-method experiment-methods experiment<- experiment<-,MultimodalExperiment-method singleCellExperiments singleCellExperiments,MultimodalExperiment-method singleCellExperiments<- singleCellExperiments<-,MultimodalExperiment-method
MultimodalExperiment Map Methods	joinMaps joinMaps,MultimodalExperiment-method map-methods
MultimodalExperiment Constructor Function	MultimodalExperiment
MultimodalExperiment Class Definition	MultimodalExperiment-class
MultimodalExperiment Name Methods	colnames colnames,MultimodalExperiment-method colnames<- colnames<-,MultimodalExperiment,ANY-method dimnames dimnames,MultimodalExperiment-method dimnames<- dimnames<-,MultimodalExperiment,ANY-method experimentNames experimentNames,MultimodalExperiment-method experimentNames<- experimentNames<-,MultimodalExperiment-method name-methods names names,MultimodalExperiment-method names<- names<-,MultimodalExperiment-method rownames rownames,MultimodalExperiment-method rownames<- rownames<-,MultimodalExperiment-method
MultimodalExperiment Slot Methods	cellData cellData,MultimodalExperiment-method cellData<- cellData<-,MultimodalExperiment-method cellMap cellMap,MultimodalExperiment-method cellMap<- cellMap<-,MultimodalExperiment-method experimentData experimentData,MultimodalExperiment-method experimentData<- experimentData<-,MultimodalExperiment-method experimentMap experimentMap,MultimodalExperiment-method experimentMap<- experimentMap<-,MultimodalExperiment-method experiments experiments,MultimodalExperiment-method experiments<- experiments<-,MultimodalExperiment-method sampleData sampleData,MultimodalExperiment-method sampleData<- sampleData<-,MultimodalExperiment-method sampleMap sampleMap,MultimodalExperiment-method sampleMap<- sampleMap<-,MultimodalExperiment-method slot-methods subjectData subjectData,MultimodalExperiment-method subjectData<- subjectData<-,MultimodalExperiment-method subjectMap subjectMap,MultimodalExperiment-method subjectMap<- subjectMap<-,MultimodalExperiment-method
MultimodalExperiment Subset Methods	subset-methods [ [,MultimodalExperiment,ANY,ANY,ANY-method [<- [<-,MultimodalExperiment,ANY,ANY,ANY-method

Package: MultimodalExperiment 1.13.0

MultimodalExperiment: Integrative Bulk and Single-Cell Experiment Container

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