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SingleCellMultiModal

Integrating Multi-modal Single Cell Experiment datasets


Bioconductor version: Release (3.18)

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], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut]

Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("SingleCellMultiModal")

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("SingleCellMultiModal")
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 HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData
Version 1.14.0
License Artistic-2.0
Depends R (>= 4.2.0), MultiAssayExperiment
Imports AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
System Requirements
URL
Bug Reports https://github.com/waldronlab/SingleCellMultiModal/issues
See More
Suggests BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me decontX, MuData
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SingleCellMultiModal_1.14.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/SingleCellMultiModal
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SingleCellMultiModal
Package Short Url https://bioconductor.org/packages/SingleCellMultiModal/
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