DEsingle
This is the development version of DEsingle; for the stable release version, see DEsingle.
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Bioconductor version: Development (3.24)
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")):
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("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 | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 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_1.33.0.tar.gz |
| Windows Binary (x86_64) | DEsingle_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | DEsingle_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | DEsingle_1.33.0.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 |