Welcome to the new bioconductor.org!

scDDboost

This is the development version of scDDboost; for the stable release version, see scDDboost.

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


Bioconductor version: Development (3.19)

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>

Citation (from within R, enter citation("scDDboost")):

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
scDDboost Tutorial HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.5.0
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
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
System Requirements c++11
URL https://github.com/wiscstatman/scDDboost
Bug Reports https://github.com/wiscstatman/scDDboost/issues
See More
Suggests knitr, rmarkdown, BiocStyle, testthat
Linking To Rcpp, RcppEigen, 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 scDDboost_1.5.0.tar.gz
Windows Binary scDDboost_1.5.0.zip
macOS Binary (x86_64) scDDboost_1.5.0.tgz
macOS Binary (arm64) scDDboost_1.5.0.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