slalom
This is the development version of slalom; for the stable release version, see slalom.
All Bioconductor versions of slalom
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Bioconductor version: 3.24 · Package version: 1.35.0
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.
Author: Florian Buettner [aut], Naruemon Pratanwanich [aut], Davis McCarthy [aut, cre], John Marioni [aut], Oliver Stegle [aut]
Maintainer: Davis McCarthy <davis at ebi.ac.uk>
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 1.35.0, https://bioconductor.org/packages/slalom.
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("slalom")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.35.0 |
| License | GPL-2 |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.6 (R-3.4) (8 years) |
| Downloads rank | 2209 of 2,456 |
| Source branch | devel |
| 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/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("slalom")| Introduction to slalom | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | slalom_1.35.0.tar.gz |
| Windows binary (x86_64) | slalom_1.35.0.zip |
| Source Repository | git clone https://git.bioconductor.org/packages/slalom |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/slalom |
| Package Downloads Report | Download Stats |
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