DSS
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see DSS.
Dispersion shrinkage for sequencing data
Bioconductor version: 3.16
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("DSS")):
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")| The DSS User's Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, DifferentialExpression, DifferentialMethylation, GeneExpression, RNASeq, Sequencing, Software |
| Version | 2.46.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | DeMixT |
| Imports Me | borealis, DMRcate, kissDE, metaseqR2, MethCP, 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_2.46.0.tar.gz |
| Windows Binary | DSS_2.46.0.zip (64-bit only) |
| macOS Binary (x86_64) | DSS_2.46.0.tgz |
| macOS Binary (arm64) | DSS_2.46.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |