SingleCellMultiModal

DOI: 10.18129/B9.bioc.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>

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	1.14.0
License	Artistic-2.0
Depends	R (>= 4.2.0), MultiAssayExperiment
Imports	AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
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	decontX, MuData
Links To Me
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/
Package Downloads Report	Download Stats