To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DSS")
In most cases, you don't need to download the package archive at all.
DSS
Dispersion shrinakge for sequencing data.
Bioconductor version: 2.14
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>
Maintainer: Hao Wu <hao.wu at emory.edu>
Citation (from within R,
enter citation("DSS")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("DSS")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DSS")
| R Script | Differential expression for RNA-seq data with dispersion shrinkage | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | ChIPSeq, DNAMethylation, DifferentialExpression, RNASeq, Sequencing, Software |
| Version | 2.2.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) |
| License | GPL |
| Depends | Biobase, locfdr |
| Imports | methods, bsseq, edgeR |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | compcodeR |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | DSS_2.2.0.tar.gz |
| Windows Binary | DSS_2.2.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | DSS_2.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | DSS_2.2.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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