DSS

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see DSS.

Dispersion shrinkage for sequencing data

Bioconductor version: 3.21

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")):

Installation

To install this package, start R (version "4.5") 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")

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 2.56.0

In Bioconductor since BioC 2.11 (R-2.15) (13 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 DeMixT

Imports Me borealis, kissDE, metaseqR2, methylSig

Suggests Me biscuiteer, methrix, NanoMethViz

Links To Me

Build Report Build Report

Package Archives

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

Source Package DSS_2.56.0.tar.gz

Windows Binary (x86_64) DSS_2.56.0.zip

macOS Binary (x86_64) DSS_2.56.0.tgz

macOS Binary (arm64) DSS_2.56.0.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/

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