SingleCellMultiModal

DOI: 10.18129/B9.bioc.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 (3.13)

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], 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 "4.1") and enter:

if (!requireNamespace("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")

 

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
PDF   Reference Manual
Text   NEWS

Details

biocViews ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData
Version 1.3.33
License Artistic-2.0
Depends R (>= 4.1.0), MultiAssayExperiment
Imports AnnotationHub, BiocFileCache, BiocGenerics, 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
Links To Me
Build Report  

Package Archives

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

Source Package SingleCellMultiModal_1.3.33.tar.gz
Windows Binary
macOS 10.13 (High Sierra)
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

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