SingleCellMultiModal
This is the development version of SingleCellMultiModal; for the stable release version, see SingleCellMultiModal.
Integrating Multi-modal Single Cell Experiment datasets
Bioconductor version: Development (3.24)
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. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
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], NCI [fnd] (GrantNo.: U24CA289073)
Maintainer: Marcel Ramos <marcel.ramos at sph.cuny.edu>
citation("SingleCellMultiModal")):Marcel Ramos, Ricard Argelaguet, Dario Righelli, Kelly Eckenrode, Ludwig Geistlinger, Levi Waldron. SingleCellMultiModal: Integrating Multi-modal Single Cell Experiment datasets. doi:10.18129/B9.bioc.SingleCellMultiModal, R package version 1.25.3, https://bioconductor.org/packages/SingleCellMultiModal.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.25.3 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| 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, StabMap |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SingleCellMultiModal_1.25.3.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/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 |