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 | decontX, MuData |
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 | |
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 |