DOI: 10.18129/B9.bioc.SingleCellMultiModal  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SingleCellMultiModal.

Integrating Multi-modal Single Cell Experiment datasets

Bioconductor version: 3.17

SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis.

Author: Marcel Ramos [aut, cre] , Ricard Argelaguet [aut], Dario Righelli [aut], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut]

Maintainer: Marcel Ramos <marcel.ramos at>

Citation (from within R, enter citation("SingleCellMultiModal")):


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HTML R Script CITEseq Cord Blood
HTML R Script ECCITEseq Peripheral Blood
HTML R Script GT-seq Mouse Embryo
HTML R Script scMultiome 10x PBMC
HTML R Script scNMT Mouse Gastrulation
HTML R Script SCoPE2: macrophage vs monocytes
HTML R Script seqFISH Mouse Visual Cortex
HTML R Script SingleCellMultiModal Introduction
PDF   Reference Manual
Text   NEWS


biocViews ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData
Version 1.12.3
License Artistic-2.0
Depends R (>= 4.2.0), MultiAssayExperiment
Imports AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
Suggests BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot
Depends On Me
Imports Me
Suggests Me MuData
Links To Me
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