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slalom

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


Bioconductor version: Release (3.18)

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")):

Installation

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


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

BiocManager::install("slalom")

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

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 PDF
NEWS Text

Details

biocViews DimensionReduction, GeneExpression, ImmunoOncology, KEGG, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.24.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-2
Depends R (>= 4.0)
Imports Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats
System Requirements
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Suggests BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
Linking To Rcpp, RcppArmadillo, BH
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Package Archives

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

Source Package slalom_1.24.0.tar.gz
Windows Binary slalom_1.24.0.zip (64-bit only)
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/slalom
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/slalom
Bioc Package Browser https://code.bioconductor.org/browse/slalom/
Package Short Url https://bioconductor.org/packages/slalom/
Package Downloads Report Download Stats