slalom
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Bioconductor version: 3.23 · Package version: 1.34.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("slalom")Details
| Maintainer | Davis McCarthy <davis@ebi.ac.uk> |
| Author | Florian Buettner [aut], Naruemon Pratanwanich [aut], Davis McCarthy [aut, cre], John Marioni [aut], Oliver Stegle [aut] |
| License | GPL-2 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DimensionReduction, GeneExpression, ImmunoOncology, KEGG, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Package Short Url | https://bioconductor.org/packages/slalom/ |
Citation
From within R, enter citation("slalom"):
Florian Buettner, Naruemon Pratanwanich, Davis McCarthy, John Marioni, Oliver Stegle. slalom: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data. doi:10.18129/B9.bioc.slalom, R package version 1.34.0, https://bioconductor.org/packages/slalom.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | slalom_1.34.0.tar.gz |
| Windows binary (x86_64) | slalom_1.34.0.zip |
Dependencies
Depends: R (>= 4.0)
Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats
LinkingTo: Rcpp, RcppArmadillo, BH
Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat