SingleCellMultiModal

DOI: 10.18129/B9.bioc.SingleCellMultiModal    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see SingleCellMultiModal.

Integrating Multi-modal Single Cell Experiment datasets

Bioconductor version: 3.12

SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. The current focus is on datasets that use new technologies such as scNMT and scM&T.

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("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	PBMC 10x multiome
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	1.2.4
License	Artistic-2.0
Depends	R (>= 4.0.0), MultiAssayExperiment
Imports	AnnotationHub, BiocFileCache, BiocGenerics, ExperimentHub, HCAMatrixBrowser, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils
LinkingTo
Suggests	knitr, scran
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_1.2.4.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