DSS

This is the development version of DSS; for the stable release version, see DSS.

Dispersion shrinkage for sequencing data

Bioconductor version: Development (3.24)

DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

Author: Hao Wu<hao.wu at emory.edu>, Hao Feng<hxf155 at case.edu>

Maintainer: Hao Wu <hao.wu at emory.edu>, Hao Feng <hxf155 at case.edu>

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

Seminal Bioconductor project articles:

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("DSS")

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("DSS")

The DSS User's Guide	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software
Version	2.61.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	GPL
Depends	R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
Imports	utils, graphics, stats, splines
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, edgeR
Linking To
Enhances
Depends On Me
Imports Me	borealis, kissDE, metaseqR2, methylSig
Suggests Me	methrix
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DSS_2.61.0.tar.gz
Windows Binary (x86_64)	DSS_2.61.0.zip
macOS Binary (big-sur-x86_64)	DSS_2.61.0.tgz
macOS Binary (sonoma-arm64)	DSS_2.61.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DSS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DSS
Bioc Package Browser	https://code.bioconductor.org/browse/DSS/
Package Short Url	https://bioconductor.org/packages/DSS/
Package Downloads Report	Download Stats