Package: slalom Type: Package Title: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data Version: 1.35.0 Date: 2025-10-14 Authors@R: c(person("Florian", "Buettner", role=c("aut"), email="buettner@ebi.ac.uk"), person("Naruemon", "Pratanwanich", role=c("aut"), email="np394@ebi.ac.uk"), person("Davis", "McCarthy", role=c("aut", "cre"), email="davis@ebi.ac.uk"), person("John", "Marioni", role = c("aut"), email="marioni@ebi.ac.uk"), person("Oliver", "Stegle", role = c("aut"), email="stegle@ebi.ac.uk")) Description: 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. Depends: R (>= 4.0) Imports: Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats Suggests: BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat LinkingTo: Rcpp, RcppArmadillo, BH License: GPL-2 VignetteBuilder: knitr LazyData: true Encoding: UTF-8 biocViews: ImmunoOncology, SingleCell, RNASeq, Normalization, Visualization, DimensionReduction, Transcriptomics, GeneExpression, Sequencing, Software, Reactome, KEGG RoxygenNote: 6.0.1 Config/pak/sysreqs: libpng-dev libxml2-dev libssl-dev zlib1g-dev Repository: https://bioc.r-universe.dev Date/Publication: 2026-04-28 12:46:38 UTC RemoteUrl: https://github.com/bioc/slalom RemoteRef: HEAD RemoteSha: 385662f0760d934b50c0e10adb5b732e044981d1 NeedsCompilation: yes Packaged: 2026-06-16 07:14:55 UTC; root Author: Florian Buettner [aut], Naruemon Pratanwanich [aut], Davis McCarthy [aut, cre], John Marioni [aut], Oliver Stegle [aut] Maintainer: Davis McCarthy