DEsingle
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Bioconductor version: 3.23 · Package version: 1.32.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DEsingle")Details
| Maintainer | Zhun Miao <miaoz13@tsinghua.org.cn> |
| Author | Zhun Miao <miaoz13@tsinghua.org.cn> |
| License | GPL-2 |
| URL | https://miaozhun.github.io/DEsingle/ |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Package Short Url | https://bioconductor.org/packages/DEsingle/ |
Citation
From within R, enter citation("DEsingle"):
Zhun Miao. DEsingle: DEsingle for detecting three types of differential expression in single-cell RNA-seq data. doi:10.18129/B9.bioc.DEsingle, R package version 1.32.0, https://bioconductor.org/packages/DEsingle.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | DEsingle_1.32.0.tar.gz |
| Windows binary (x86_64) | DEsingle_1.32.0.zip |
| macOS binary (arm64) | DEsingle_1.32.0.tgz |
| macOS binary (x86_64) | DEsingle_1.32.0.tgz |
Dependencies
Depends: R (>= 3.4.0)
Imports: stats, Matrix (>= 1.2-14), MASS (>= 7.3-45), VGAM (>= 1.0-2), bbmle (>= 1.0.18), gamlss (>= 4.4-0), maxLik (>= 1.3-4), pscl (>= 1.4.9), BiocParallel (>= 1.12.0)
Suggests: knitr, rmarkdown, SingleCellExperiment