slalom

DOI: 10.18129/B9.bioc.slalom  

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

Bioconductor version: Release (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>

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")

 

HTML	R Script	Introduction to slalom
PDF		Reference Manual
Text		NEWS

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) (5.5 years)
License	GPL-2
Depends	R (>= 4.0)
Imports	Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats
LinkingTo	Rcpp, RcppArmadillo, BH
Suggests	BiocStyle, knitr, rhdf5, rmarkdown, scater, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
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