slalom
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Bioconductor version: Release (3.19)
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. The method uses Bayesian factor analysis with a latent variable model to identify active pathways (selected by the user, e.g. KEGG pathways) that explain variation in a single-cell RNA-seq dataset. This an R/C++ implementation of the f-scLVM Python package. See the publication describing the method at https://doi.org/10.1186/s13059-017-1334-8.
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 "4.4") 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, KEGG, Normalization, RNASeq, Reactome, Sequencing, SingleCell, Software, Transcriptomics, Visualization |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | GPL-2 |
| Depends | R (>= 4.0) |
| Imports | Rcpp (>= 0.12.8), RcppArmadillo, BH, ggplot2, grid, GSEABase, methods, rsvd, SingleCellExperiment, SummarizedExperiment, stats |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rhdf5, rmarkdown, 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_1.26.0.tar.gz |
| Windows Binary (x86_64) | slalom_1.26.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |