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scMultiome

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

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


Bioconductor version: Development (3.20)

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] , Aleksander Chlebowski [aut], Aaron Lun [aut], Shiqi Xie [ctb], Tomasz Włodarczyk [aut]

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

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
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

Details

biocViews CellCulture, ExperimentData, ExperimentHub, ExpressionData, GEO, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue
Version 1.5.0
License CC BY-SA 4.0
Depends AnnotationHub, ExperimentHub(>= 2.8.1), MultiAssayExperiment, SingleCellExperiment, SummarizedExperiment
Imports AzureStor, DelayedArray, GenomicRanges, HDF5Array, S4Vectors, checkmate, methods, rhdf5
System Requirements
URL
See More
Suggests BiocGenerics, IRanges, Matrix, knitr, rmarkdown, rstudioapi, testthat (>= 3.0.0), devtools, BiocStyle, ExperimentHubData
Linking To
Enhances
Depends On Me
Imports Me epiregulon
Suggests Me epiregulon.extra
Links To Me
Build Report Build Report

Package Archives

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

Source Package scMultiome_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (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