scDDboost

DOI: 10.18129/B9.bioc.scDDboost  

A compositional model to assess expression changes from single-cell rna-seq data

Bioconductor version: Release (3.17)

scDDboost is an R package to analyze changes in the distribution of single-cell expression data between two experimental conditions. Compared to other methods that assess differential expression, scDDboost benefits uniquely from information conveyed by the clustering of cells into cellular subtypes. Through a novel empirical Bayesian formulation it calculates gene-specific posterior probabilities that the marginal expression distribution is the same (or different) between the two conditions. The implementation in scDDboost treats gene-level expression data within each condition as a mixture of negative binomial distributions.

Author: Xiuyu Ma [cre, aut], Michael A. Newton [ctb]

Maintainer: Xiuyu Ma <watsonforfun at gmail.com>

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scDDboost")

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("scDDboost")

 

HTML	R Script	scDDboost Tutorial
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	GPL (>= 2)
Depends	R (>= 4.2), ggplot2
Imports	Rcpp (>= 0.12.11), RcppEigen (>= 0.3.2.9.0), EBSeq, BiocParallel, mclust, SingleCellExperiment, cluster, Oscope, SummarizedExperiment, stats, methods
LinkingTo	Rcpp, RcppEigen, BH
Suggests	knitr, rmarkdown, BiocStyle, testthat
SystemRequirements	c++11
Enhances
URL	https://github.com/wiscstatman/scDDboost
BugReports	https://github.com/wiscstatman/scDDboost/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	scDDboost_1.2.0.tar.gz
Windows Binary	scDDboost_1.2.0.zip
macOS Binary (x86_64)	scDDboost_1.2.0.tgz
macOS Binary (arm64)	scDDboost_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scDDboost
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scDDboost
Bioc Package Browser	https://code.bioconductor.org/browse/scDDboost/
Package Short Url	https://bioconductor.org/packages/scDDboost/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive