DEsingle
This package is for version 3.7 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: 3.7
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("DEsingle")
):
Installation
To install this package, start R (version "3.5") 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, Preprocessing, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
Version | 1.0.5 |
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_1.0.5.tar.gz |
Windows Binary | DEsingle_1.0.5.zip |
Mac OS X 10.11 (El Capitan) | DEsingle_1.0.5.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 3.7 | Source Archive |