The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNAseq 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 pergene 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@purdue.edu>, Wolfgang Huber <whuber@embl.de> and Olga Vitek <ovitek@purdue.edu> 
Bioconductor views  RNASeq 
Date of publication  None 
Maintainer  Danni Yu <dyu@purdue.edu> 
License  GPL (>= 3) 
Version  1.14.0 
Package repository  View on Bioconductor 
Installation  Install the latest version of this package by entering the following in R:



All man pages Function index File listing
Man pages  

countsTable: An Example Simulation Data  
drawMA_vol: Draw MA Plot and Volcano Plot  
ecdfAUC: Draw Empirical Cumulative Density Function (ECDF) plot  
equalSpace: Calculate Grouped Shrinkage Estimates  
exactNBtest1: Perform only one exact test under the Negative Binomial...  
getAdjustDisp: Calculate Shrinkage (SH) Estimates for Dispersion  
getNormFactor: Estimate size factors  
getQ: Estimate the shrinkage target based on the quantiles of...  
getT: Estimate the shrinkage target based on the initial estimates  
getTgroup: This is an internal function used to calculate the shrinkage...  
Hammer2months: An example of real experiment.  
nbinomTestForMatricesSH: Exact test under Negative Binomial Test with Shrinkage...  
nbTestSH: Differential Analysis based on RNAseq experiments using...  
plotDispersion: Drawing DispersionMean plot.  
rnbinomMV: Randomly Generate Negative Binomial Variable with parameters...  
rowVars: Calculating the sample variance within each row of A matrix  
sim: Generating Simulated Data  
sSeqpackage: Shrinkage estimation of dispersion in Negative Binomial...  
Sultan: An example of real experiment.  
Tuch: An example of real experiment. 
Functions  

Hammer2months  Man page 
Sultan  Man page 
Tuch  Man page 
countsTable  Man page 
drawMA_vol  Man page Source code 
ecdfAUC  Man page Source code 
equalSpace  Man page Source code 
exactNBtest1  Man page Source code 
getAdjustDisp  Man page Source code 
getNormFactor  Man page Source code 
getQ  Man page Source code 
getT  Man page Source code 
getTgroup  Man page Source code 
nbTestSH  Man page Source code 
nbinomTestForMatricesSH  Man page Source code 
plotDispersion  Man page Source code 
rnbinomMV  Man page Source code 
rowVars  Man page Source code 
sSeq  Man page 
sSeqpackage  Man page 
sim  Man page Source code 
Files  

DESCRIPTION
 
NAMESPACE
 
R
 
R/drawMA_vol.R  
R/ecdfAUC.R  
R/equalSpace.R  
R/exactNBtest1.R  
R/getAdjustDisp.R  
R/getNormFactor.R  
R/getQ.R  
R/getT.R  
R/getTgroup.R  
R/nbTestSH.R  
R/nbinomTestForMatricesSH.R  
R/plotDispersion.R  
R/rnbinomMV.R  
R/rowVars.R  
R/sim.R  
build
 
build/vignette.rds
 
data
 
data/Hammer2months.rda
 
data/Sultan.rda
 
data/Tuch.rda
 
data/countsTable.rda
 
inst
 
inst/doc
 
inst/doc/sSeq.R  
inst/doc/sSeq.Rnw
 
inst/doc/sSeq.pdf
 
man
 
man/Hammer2months.Rd  
man/Sultan.Rd  
man/Tuch.Rd  
man/countsTable.Rd  
man/drawMA_vol.Rd  
man/ecdfAUC.Rd  
man/equalSpace.Rd  
man/exactNBtest1.Rd  
man/getAdjustDisp.Rd  
man/getNormFactor.Rd  
man/getQ.Rd  
man/getT.Rd  
man/getTgroup.Rd  
man/nbTestSH.Rd  
man/nbinomTestForMatricesSH.Rd  
man/plotDispersion.Rd  
man/rnbinomMV.Rd  
man/rowVars.Rd  
man/sSeqpackage.Rd  
man/sim.Rd  
vignettes
 
vignettes/sSeq.Rnw
 
vignettes/sSeq.bib

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