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DSS

Dispersion shrinkage for sequencing data


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software
Version 2.50.1
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License GPL
Depends R (>= 3.5.0), methods, Biobase, BiocParallel, bsseq, parallel
Imports utils, graphics, stats, splines
System Requirements
URL
See More
Suggests BiocStyle, knitr, rmarkdown, edgeR
Linking To
Enhances
Depends On Me DeMixT
Imports Me borealis, kissDE, metaseqR2, methylSig
Suggests Me biscuiteer, methrix, NanoMethViz, PROPER
Links To Me
Build Report Build Report

Package Archives

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

Source Package DSS_2.50.1.tar.gz
Windows Binary DSS_2.50.1.zip
macOS Binary (x86_64) DSS_2.50.1.tgz
macOS Binary (arm64) DSS_2.50.1.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