SingleCellMultiModal
Integrating Multi-modal Single Cell Experiment datasets
Bioconductor version: Release (3.19)
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], Al Abadi [ctb], Dario Righelli [aut], Christophe Vanderaa [ctb], Kelly Eckenrode [aut], Ludwig Geistlinger [aut], Levi Waldron [aut]
Maintainer: Marcel Ramos <marcel.ramos at roswellpark.org>
citation("SingleCellMultiModal")):
Installation
To install this package, start R (version "4.4") 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.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("SingleCellMultiModal")| 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 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentData, ExperimentHub, GEO, ReproducibleResearch, SingleCellData |
| Version | 1.16.0 |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0), MultiAssayExperiment |
| Imports | AnnotationHub, BiocBaseUtils, BiocFileCache, ExperimentHub, graphics, HDF5Array, S4Vectors, SingleCellExperiment, SpatialExperiment, SummarizedExperiment, Matrix, methods, utils |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/waldronlab/SingleCellMultiModal/issues |
See More
| Suggests | BiocStyle, ggplot2, knitr, RaggedExperiment, rmarkdown, scater, scran, UpSetR, uwot |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | MuData, decontX |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleCellMultiModal_1.16.0.tar.gz |
| Windows Binary (x86_64) | |
| 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 |