scDDboost

DOI: 10.18129/B9.bioc.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 (3.17)

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>

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

Installation

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

 

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PDF   Reference Manual
Text   NEWS

Details

biocViews Bayesian, Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software
Version 1.1.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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
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Build Report  

Package Archives

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

Source Package scDDboost_1.1.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/scDDboost
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scDDboost
Package Short Url https://bioconductor.org/packages/scDDboost/
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