Package: slalom
Type: Package
Title: Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Version: 1.33.0
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: 2025-10-29 14:41:26 UTC
RemoteUrl: https://github.com/bioc/slalom
RemoteRef: HEAD
RemoteSha: 42126fd645bc1b682635f91ad04db1e754532286
NeedsCompilation: yes
Packaged: 2026-03-04 09:28:51 UTC; root
Author: Florian Buettner [aut],
  Naruemon Pratanwanich [aut],
  Davis McCarthy [aut, cre],
  John Marioni [aut],
  Oliver Stegle [aut]
Maintainer: Davis McCarthy <davis@ebi.ac.uk>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-03-09 11:05:33 UTC; windows
Archs: x64
