SingleCellMultiModal

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see SingleCellMultiModal.

Integrating Multi-modal Single Cell Experiment datasets

DOI: 10.18129/B9.bioc.SingleCellMultiModal

Bioconductor version: 3.16

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 roswellpark.org>

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

Installation

To install this package, start R (version "4.2") 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

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData

Version 1.10.1

License Artistic-2.0

Depends R (>= 4.2.0), MultiAssayExperiment

Imports AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils

System Requirements

URL

Bug Reports https://github.com/waldronlab/SingleCellMultiModal/issues

Suggests BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me MuData

Links To Me

Build Report Build Report

Package Archives

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

Source Package SingleCellMultiModal_1.10.1.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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