SingleCellMultiModal

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 roswellpark.org>

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")

 

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

Details

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
LinkingTo
Suggests	BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot
SystemRequirements
Enhances
URL
BugReports	https://github.com/waldronlab/SingleCellMultiModal/issues
Depends On Me
Imports Me
Suggests Me	MuData
Links To Me
Build Report

Package Archives

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

Source Package	SingleCellMultiModal_1.12.3.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/
Package Downloads Report	Download Stats