sSeq (version 1.10.0)

sSeq-package: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Description

This package is to discover the genes that differentially expressed between two conditions based on RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are simply shrunk toward a target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions are not different.

Details

Package:

sSeq

Type:

Package

Version:

1.0

Date:

2013-02-25

References

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size

Examples

#load a simulated data that includes a count table
data("countsTable")

#calculate the p-values using the shrinkage approach.
conds <- c("A", "B")
resJS <- nbTestSH( countsTable, conds, "A", "B")