scMultiome

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17

Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets

Bioconductor version: Development (3.24)

Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR package and presented as MultiAssayExperiment objects.

Author: Xiaosai Yao [cre, aut] ORCID: 0000-0001-9729-0726 , Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut] ORCID: 0000-0003-1554-9699

Maintainer: Xiaosai Yao <xiaosai.yao at gmail.com>

Citation (from within R, enter citation("scMultiome")):

Xiaosai Yao, Aleksander Chlebowski, Aaron Lun, Tomasz Włodarczyk. scMultiome: Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets. doi:10.18129/B9.bioc.scMultiome, R package version 1.13.2, https://bioconductor.org/packages/scMultiome.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

BiocManager::install("scMultiome")

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("scMultiome")

scMultiome tutorial	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CellCulture, ExperimentData, ExperimentHub, ExpressionData, GEO, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue
Version	1.13.2
In Bioconductor since	BioC 3.17 (R-4.3) (3.5 years)
License	CC BY-SA 4.0
Depends	AnnotationHub, ExperimentHub (>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment
Imports	AzureStor, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5, alabaster.matrix
System Requirements
URL

Suggests	BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	epiregulon, epiregulon.extra
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	scMultiome_1.13.2.tar.gz
Windows Binary (x86_64)
macOS Binary (big-sur-x86_64)
macOS Binary (sonoma-arm64)
Source Repository	git clone https://git.bioconductor.org/packages/scMultiome
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scMultiome
Package Short Url	https://bioconductor.org/packages/scMultiome/
Package Downloads Report	Download Stats