DOI: 10.18129/B9.bioc.sSeq    

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see sSeq.

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

Bioconductor version: 3.14

The purpose of this package is to discover the genes that are differentially expressed between two conditions in 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 shrunk towards an estimated 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 identically follow a NB distribution.

Author: Danni Yu <dyu at>, Wolfgang Huber <whuber at> and Olga Vitek <ovitek at>

Maintainer: Danni Yu <dyu at>

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PDF R Script sSeq
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biocViews ImmunoOncology, RNASeq, Software
Version 1.32.0
In Bioconductor since BioC 2.13 (R-3.0) (8.5 years)
License GPL (>= 3)
Depends R (>= 3.0), caTools, RColorBrewer
Depends On Me
Imports Me MLSeq
Suggests Me NBLDA
Links To Me
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