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DSS (version 2.12.0)

Dispersion shrinakge for sequencing data.

Description

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.

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Version

Version

2.12.0

License

GPL

Maintainer

Last Published

February 15th, 2017

Functions in DSS (2.12.0)

normalizationFactor

Accessor functions for the 'normalizationFactor' slot in a SeqCountData object.

Function to perform statistical test of differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.

Function to detect differntially methylated loci (DML) for two group comparisons of bisulfite sequencing (BS-seq) data.

Perform gene-wise Wald test for two group comparisons for sequencing count data.

DMLtest.multiFactor

Perform statistical test for BS-seq data from general experimental design

Dispersion shrinkage for sequencing data

Acessor functions for the 'dispersion' slot in a SeqCountData object.

A simulated 'SeqCountData' object.

Perform RNA-seq differential expression analysis in two-group comparison

Create an object of BSseq class from several data frames.

Estimate normalization factors

Estimate and shrink tag-specific dipsersions

DMLfit.multiFactor

Fit a linear model for BS-seq data from general experimental design

Function to detect differntially methylated regions (DMR) for two group comparisons of bisulfite sequencing (BS-seq) data.

Visualze the count data for one DMR

SeqCountSet-class

Class "SeqCountSet" - container for count data from sequencing experiment