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

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.

AuthorDanni Yu <dyu@purdue.edu>, Wolfgang Huber <whuber@embl.de> and Olga Vitek <ovitek@purdue.edu>
Date of publicationNone
MaintainerDanni Yu <dyu@purdue.edu>
LicenseGPL (>= 3)
Version1.12.0

View on Bioconductor

Functions

countsTable Man page
drawMA_vol Man page
ecdfAUC Man page
equalSpace Man page
exactNBtest1 Man page
getAdjustDisp Man page
getNormFactor Man page
getQ Man page
getT Man page
getTgroup Man page
Hammer2months Man page
nbinomTestForMatricesSH Man page
nbTestSH Man page
plotDispersion Man page
rnbinomMV Man page
rowVars Man page
sim Man page
sSeq Man page
sSeq-package Man page
Sultan Man page
Tuch Man page

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