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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.15.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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++14 |
| 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_1.15.0.tar.gz |
| Windows Binary (x86_64) | scDDboost_1.15.0.zip |
| macOS Binary (big-sur-x86_64) | scDDboost_1.15.0.tgz |
| macOS Binary (sonoma-arm64) | scDDboost_1.15.0.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 |