slalom

DOI: 10.18129/B9.bioc.slalom    

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

Bioconductor version: Release (3.6)

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 and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("slalom")

Documentation

HTML	R Script	Introduction to slalom
PDF		Reference Manual
Text		NEWS

Details

biocViews	DimensionReduction, GeneExpression, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization
Version	1.0.0
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
Build Report

Package Archives

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

Source Package	slalom_1.0.0.tar.gz
Windows Binary	slalom_1.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	slalom_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/slalom
Package Short Url	http://bioconductor.org/packages/slalom/
Package Downloads Report	Download Stats