slalom
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see slalom.
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Bioconductor version: 3.9
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 "3.6") 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 | 1.6.0 |
| 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_1.6.0.tar.gz |
| Windows Binary | slalom_1.6.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | slalom_1.6.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/slalom |
| Source Repository (Developer Access) | git clone [email protected]: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 3.9 | Source Archive |