DSS

DOI: 10.18129/B9.bioc.DSS    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DSS.

Dispersion shrinkage for sequencing data

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

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

Details

biocViews	DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software
Version	2.44.0
In Bioconductor since	BioC 2.11 (R-2.15) (10 years)
License	GPL
Depends	R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
Imports	utils, graphics, stats, splines, matrixStats
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	borealis, DMRcate, kissDE, metaseqR2, MethCP, methylSig
Suggests Me	biscuiteer, methrix, NanoMethViz, PROPER
Links To Me
Build Report

Package Archives

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

Source Package	DSS_2.44.0.tar.gz
Windows Binary	DSS_2.44.0.zip
macOS Binary (x86_64)	DSS_2.44.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DSS
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DSS
Package Short Url	https://bioconductor.org/packages/DSS/
Package Downloads Report	Download Stats