SingleCellMultiModal

This is the development version of SingleCellMultiModal; for the stable release version, see SingleCellMultiModal.

Integrating Multi-modal Single Cell Experiment datasets

Bioconductor version: Development (3.21)

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. To cite, use the 'citation' function and see .

Author: Marcel Ramos [aut, cre] (ORCID: ), 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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData
Version	1.19.1
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

Suggests	BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	decontX, MuData, StabMap
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	SingleCellMultiModal_1.19.1.tar.gz
Windows Binary (x86_64)
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