DEsingle

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DEsingle.

DEsingle for detecting three types of differential expression in single-cell RNA-seq data


Bioconductor version: 3.10

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 mails.tsinghua.edu.cn>

Maintainer: Zhun Miao <miaoz13 at mails.tsinghua.edu.cn>

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

Installation

To install this package, start R (version "3.6") 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 PDF
NEWS Text

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.7 (R-3.5) (6 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_1.6.0.tar.gz
Windows Binary DEsingle_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) DEsingle_1.6.0.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
Old Source Packages for BioC 3.10 Source Archive