Bioconductor version: Release (3.17)
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], Ludwig Geistlinger [aut], Levi Waldron [aut]
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
Citation (from within R,
enter citation("SingleCellMultiModal")
):
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("SingleCellMultiModal")
For older versions of R, please refer to the appropriate Bioconductor release.
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 |
HTML | R Script | SingleCellMultiModal Introduction |
Reference Manual | ||
Text | NEWS |
biocViews | ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData |
Version | 1.12.3 |
License | Artistic-2.0 |
Depends | R (>= 4.2.0), MultiAssayExperiment |
Imports | AnnotationHub, BiocBaseUtils, BiocFileCache, 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 | MuData |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | SingleCellMultiModal_1.12.3.tar.gz |
Windows Binary | |
macOS Binary (x86_64) | |
macOS Binary (arm64) | |
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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