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.

Author
Danni Yu <dyu@purdue.edu>, Wolfgang Huber <whuber@embl.de> and Olga Vitek <ovitek@purdue.edu>
Date of publication
None
Maintainer
Danni Yu <dyu@purdue.edu>
License
GPL (>= 3)
Version
1.12.0

View on Bioconductor

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.

Files in this package

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