scMultiome
This is the released version of scMultiome; for the devel version, see scMultiome.
Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets
Bioconductor version: Release (3.23)
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("scMultiome")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | ||
| NEWS | Text |
Details
| biocViews | CellCulture, ExperimentData, ExperimentHub, ExpressionData, GEO, Homo_sapiens_Data, PackageTypeData, SequencingData, SingleCellData, Tissue |
| Version | 1.12.0 |
| 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 |
See More
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scMultiome_1.12.0.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 |