sSeq: Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size
Version 1.14.0

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>
Bioconductor views RNASeq
Date of publicationNone
MaintainerDanni Yu <dyu@purdue.edu>
LicenseGPL (>= 3)
Version1.14.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("sSeq")

Getting started

Package overview

Popular man pages

drawMA_vol: Draw MA Plot and Volcano Plot
ecdfAUC: Draw Empirical Cumulative Density Function (ECDF) plot
getAdjustDisp: Calculate Shrinkage (SH) Estimates for Dispersion
nbTestSH: Differential Analysis based on RNA-seq experiments using...
rowVars: Calculating the sample variance within each row of A matrix
sSeq-package: Shrinkage estimation of dispersion in Negative Binomial...
Sultan: An example of real experiment.
See all...

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 RNA-seq experiments using...
plotDispersion: Drawing Dispersion-Mean plot.
rnbinomMV: Randomly Generate Negative Binomial Variable with parameters...
rowVars: Calculating the sample variance within each row of A matrix
sim: Generating Simulated Data
sSeq-package: 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
sSeq-package 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/sSeq-package.Rd
man/sim.Rd
vignettes
vignettes/sSeq.Rnw
vignettes/sSeq.bib
sSeq documentation built on May 20, 2017, 9:29 p.m.

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