scDD
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Bioconductor version: 3.24 · Package version: 1.37.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("scDD")Details
| Maintainer | Keegan Korthauer <keegan@stat.ubc.ca> |
| Author | Keegan Korthauer [cre, aut] (ORCID: <https://orcid.org/0000-0002-4565-1654>) |
| License | GPL-2 |
| URL | https://github.com/kdkorthauer/scDD |
| Bug Reports | https://github.com/kdkorthauer/scDD/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Bayesian, Clustering, DifferentialExpression, ImmunoOncology, MultipleComparison, RNASeq, SingleCell, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/scDD/ |
Citation
From within R, enter citation("scDD"):
Keegan Korthauer. scDD: Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions. doi:10.18129/B9.bioc.scDD, R package version 1.37.0, https://bioconductor.org/packages/scDD.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | scDD_1.37.0.tar.gz |
| Windows binary (x86_64) | scDD_1.37.0.zip |
| macOS binary (arm64) | scDD_1.37.0.tgz |
| macOS binary (x86_64) | scDD_1.37.0.tgz |
Dependencies
Depends: R (>= 3.5.0)
Imports: fields, mclust, BiocParallel, outliers, ggplot2, EBSeq, arm, SingleCellExperiment, SummarizedExperiment, grDevices, graphics, stats, S4Vectors, scran
Reverse dependencies
Suggests Me (1): splatter