slalom

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see slalom.

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


Bioconductor version: 3.16

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 "4.2") 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 1.20.2
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
URL
See More
Suggests BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
Linking To Rcpp, RcppArmadillo, BH
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package slalom_1.20.2.tar.gz
Windows Binary slalom_1.20.2.zip
macOS Binary (x86_64) slalom_1.20.2.tgz
macOS Binary (arm64) slalom_1.20.2.tgz
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
Old Source Packages for BioC 3.16 Source Archive