slalom

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.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("slalom")