slalom
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see slalom.
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Bioconductor version: 3.11
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("slalom")
):
Installation
To install this package, start R (version "4.0") 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 | ||
NEWS | Text |
Details
biocViews | DimensionReduction, GeneExpression, ImmunoOncology, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
Version | 1.10.0 |
In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
License | GPL-2 |
Depends | R (>= 3.4) |
Imports | Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats |
System Requirements | |
URL |
See More
Suggests | knitr, rhdf5, 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_1.10.0.tar.gz |
Windows Binary | slalom_1.10.0.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | slalom_1.10.0.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 3.11 | Source Archive |