DOI: 10.18129/B9.bioc.slalom  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see slalom.

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Bioconductor version: 3.17

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

Author: Florian Buettner [aut], Naruemon Pratanwanich [aut], Davis McCarthy [aut, cre], John Marioni [aut], Oliver Stegle [aut]

Maintainer: Davis McCarthy <davis at>

Citation (from within R, enter citation("slalom")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



HTML R Script Introduction to slalom
PDF   Reference Manual
Text   NEWS


biocViews DimensionReduction, GeneExpression, ImmunoOncology, KEGG, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.22.0
In Bioconductor since BioC 3.6 (R-3.4) (6 years)
License GPL-2
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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package slalom_1.22.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64) slalom_1.21.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: