slalom

DOI: 10.18129/B9.bioc.slalom    

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

Bioconductor version: Release (3.13)

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.

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 "4.1") and enter:

if (!requireNamespace("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, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.14.0
In Bioconductor since	BioC 3.6 (R-3.4) (4 years)
License	GPL-2
Depends	R (>= 3.4)
Imports	Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats
LinkingTo	Rcpp, RcppArmadillo, BH
Suggests	knitr, rhdf5, scater, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package	slalom_1.14.0.tar.gz
Windows Binary	slalom_1.14.0.zip
macOS 10.13 (High Sierra)	slalom_1.14.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/slalom
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/slalom
Package Short Url	https://bioconductor.org/packages/slalom/
Package Downloads Report	Download Stats