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 (3.21)
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("scDDboost")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Clustering, DifferentialExpression, GeneExpression, Sequencing, SingleCell, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | scDDboost_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | scDDboost_1.9.0.tgz |
| macOS Binary (arm64) | scDDboost_1.9.0.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 |