Package: MultimodalExperiment 1.7.0

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]

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MultimodalExperiment.pdf |MultimodalExperiment.html✨
MultimodalExperiment/json (API)
NEWS

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

Peer review:

Datasets:
  • pbRNAseq - MultimodalExperiment Example Data
  • scADTseq - MultimodalExperiment Example Data
  • scRNAseq - MultimodalExperiment Example Data

On BioConductor:MultimodalExperiment-1.7.0(bioc 3.21)MultimodalExperiment-1.6.0(bioc 3.20)

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

datarepresentationinfrastructuresinglecell

4.18 score 3 scripts 108 downloads 37 exports 50 dependencies

Last updated 2 months agofrom:d92c351dba. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winOKNov 29 2024
R-4.5-linuxOKNov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:bulkExperimentsbulkExperiments<-cellDatacellData<-cellMapcellMap<-colnamescolnames<-experimentexperiment<-experimentDataexperimentData<-ExperimentListexperimentMapexperimentMap<-experimentNamesexperimentNames<-experimentsexperiments<-harmonizejoinAnnotationsjoinMapsMultimodalExperimentpropagaterownamesrownames<-sampleDatasampleData<-sampleMapsampleMap<-showsingleCellExperimentssingleCellExperiments<-subjectDatasubjectData<-subjectMapsubjectMap<-

Dependencies:abindaskpassBiobaseBiocBaseUtilsBiocGenericsclicpp11crayoncurlDelayedArraydplyrfansigenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmimeMultiAssayExperimentopensslpillarpkgconfigpurrrR6rlangS4ArraysS4VectorsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrswithrXVectorzlibbioc

MultimodalExperiment

Lucas Schiffer

Rendered fromMultimodalExperiment.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
MultimodalExperiment Annotation Methodsannotation-methods joinAnnotations joinAnnotations,MultimodalExperiment-method
MultimodalExperiment Coordination Methodscoordination-methods harmonize harmonize,MultimodalExperiment-method propagate propagate,MultimodalExperiment-method
MultimodalExperiment Example Dataexample-data pbRNAseq scADTseq scRNAseq
MultimodalExperiment Experiment MethodsbulkExperiments 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 MethodsjoinMaps joinMaps,MultimodalExperiment-method map-methods
MultimodalExperiment Constructor FunctionMultimodalExperiment
MultimodalExperiment Class DefinitionMultimodalExperiment-class
MultimodalExperiment Name Methodscolnames 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 MethodscellData 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 Methodssubset-methods [ [,MultimodalExperiment,ANY,ANY,ANY-method [<- [<-,MultimodalExperiment,ANY,ANY,ANY-method