DEsingle
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Bioconductor version: Release (3.20)
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.
Author: Zhun Miao <miaoz13 at tsinghua.org.cn>
Maintainer: Zhun Miao <miaoz13 at tsinghua.org.cn>
citation("DEsingle")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("DEsingle")
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("DEsingle")| DEsingle | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6.5 years) |
| License | GPL-2 |
| 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) |
| System Requirements | |
| URL | https://miaozhun.github.io/DEsingle/ |
See More
| Suggests | knitr, rmarkdown, SingleCellExperiment |
| Linking To | |
| 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 | DEsingle_1.26.0.tar.gz |
| Windows Binary (x86_64) | DEsingle_1.26.0.zip (64-bit only) |
| macOS Binary (x86_64) | DEsingle_1.26.0.tgz |
| macOS Binary (arm64) | DEsingle_1.26.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/DEsingle |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DEsingle |
| Bioc Package Browser | https://code.bioconductor.org/browse/DEsingle/ |
| Package Short Url | https://bioconductor.org/packages/DEsingle/ |
| Package Downloads Report | Download Stats |