slalom

DOI: 10.18129/B9.bioc.slalom    

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

Bioconductor version: Release (3.8)

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>

Citation (from within R, enter citation("slalom")):

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("slalom", version = "3.8")

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, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version 1.4.0
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
Links To Me
Build Report  

Package Archives

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

Source Package slalom_1.4.0.tar.gz
Windows Binary slalom_1.4.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) slalom_1.4.0.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 http://bioconductor.org/packages/slalom/
Package Downloads Report Download Stats

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