baySeq: Empirical Bayesian analysis of patterns of differential expression in count data

This package identifies differential expression in high-throughput 'count' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

AuthorThomas J. Hardcastle
Date of publicationNone
MaintainerThomas J. Hardcastle <tjh48@cam.ac.uk>
LicenseGPL-3
Version2.8.0

View on Bioconductor

Man pages

allModels: Function to generate all possible models for a countData...

baySeq-classes: baySeq - classes

baySeq-package: Empirical Bayesian analysis of patterns of differential...

bimodalSep: A function that, given a numeric vector, finds the value...

CDPost: 'countData' object derived from data file 'simData' with...

CDPriors: 'countData' object derived from data file 'simData' with...

densityFunction: Class '"densityFunction"'

densityFunctions: Lists all currently available densityFunctions.

getLibsizes: Estimates library scaling factors (library sizes) for count...

getLikelihoods: Finds posterior likelihoods for each count or paired count as...

getPosteriors: An internal function in the baySeq package for calculating...

getPriors: Estimates prior parameters for the underlying distributions...

getTPs: Gets the number of true positives in the top n counts...

makeOrderings: Construct orderings for count data given a model structure...

marginaliseEqual: Computes marginal likelihoods that two replicate groups are...

marginalisePairwise: Computes marginal likelihoods that two replicate groups...

methObservables: Generation of intermediate values in likelihood estimation...

mobAnnotation: Annotation data for a set of small RNA loci derived from...

mobData: Data from a set of small RNA sequencing experiments carried...

pairData: Simulated data for testing the baySeq package methods for...

plotMA.CD: 'MA'-plot for count data.

plotNullPrior: Plots distribution of null function and shows the threshold...

plotPosteriors: Plots the posterior likelihoods estimated for a 'countData'...

plotPriors: Plots the density of the log values estimated for the mean...

selectTop: Selects the top genomic events, based on posterior...

simData: Simulated data for testing the baySeq package methods

summarisePosteriors: Summarises expected number of genomic events given the...

topCounts: Get the top counts corresponding to some group from a...

zimData: Simulated data for testing the baySeq package methods

Functions

allModels Man page
baySeq Man page
baySeq-class Man page
baySeq-classes Man page
baySeq-package Man page
bbDensity Man page
bbNCDist Man page
bimodalSeparator Man page
CDPost Man page
CDPriors Man page
countData Man page
[,countData,ANY-method Man page
countData-class Man page
[,countData-method Man page
densityFunction Man page
densityFunction<- Man page
densityFunction-class Man page
densityFunction<-,countData-method Man page
densityFunction,countData-method Man page
densityFunctions Man page
dim,countData-method Man page
getLibsizes Man page
getLikelihoods Man page
getLikelihoods.BB Man page
getLikelihoods.NB Man page
getPosteriors Man page
getPriors Man page
getPriors.BB Man page
getPriors.NB Man page
getTPs Man page
groups Man page
groups<- Man page
groups<-,countData-method Man page
groups,countData-method Man page
libsizes Man page
libsizes<- Man page
libsizes<-,countData-method Man page
libsizes,countData-method Man page
libsizes<-,pairedData-method Man page
libsizes,pairedData-method Man page
makeOrderings Man page
marginaliseEqual Man page
marginalisePairwise Man page
md2Density Man page
md3Density Man page
mdDensity Man page
methObservables Man page
mobAnnotation Man page
mobData Man page
nbinomDensity Man page
normDensity Man page
pairData Man page
pairedData Man page
pairedData-class Man page
[,pairedData-method Man page
plotMA.CD Man page
plotNullPrior Man page
plotPosteriors Man page
plotPriors Man page
rbind Man page
rbind,countData-method Man page
replicates Man page
replicates<- Man page
replicates<-,countData-method Man page
replicates,countData-method Man page
seglens Man page
seglens<- Man page
seglens<-,countData-method Man page
seglens,countData-method Man page
selectTop Man page
show,countData-method Man page
show,pairedData-method Man page
simData Man page
summarisePosteriors Man page
topCounts Man page
zimData Man page
ZINBDensity Man page

Files

baySeq/DESCRIPTION
baySeq/NAMESPACE
baySeq/R
baySeq/R/AllClasses.R baySeq/R/allModels.R baySeq/R/betaBinomial.R baySeq/R/bimodalSep.R baySeq/R/bimodalSeparator.R baySeq/R/countData-accessors.R baySeq/R/densDensityFunctions.R baySeq/R/densityFunction-accessors.R baySeq/R/densityFunctions.R baySeq/R/getLibsizes.R baySeq/R/getLikelihoods.NB.R baySeq/R/getLikelihoods.R baySeq/R/getPriors.LN.R baySeq/R/getPriors.R baySeq/R/getPriors_Generic.R baySeq/R/getTPs.R baySeq/R/marginalisePairwise.R baySeq/R/plotMA.CD.R baySeq/R/plotPosteriors.R baySeq/R/plotPriors.R baySeq/R/summarisePosteriors.R baySeq/R/topCounts.R baySeq/R/utilityFunctions.R
baySeq/build
baySeq/build/vignette.rds
baySeq/data
baySeq/data/CDPost.RData
baySeq/data/CDPriors.RData
baySeq/data/mobAnnotation.RData
baySeq/data/mobData.RData
baySeq/data/pairData.RData
baySeq/data/simData.RData
baySeq/data/zimData.RData
baySeq/inst
baySeq/inst/doc
baySeq/inst/doc/baySeq.R
baySeq/inst/doc/baySeq.Rnw
baySeq/inst/doc/baySeq.pdf
baySeq/inst/doc/baySeq_generic.R
baySeq/inst/doc/baySeq_generic.Rnw
baySeq/inst/doc/baySeq_generic.pdf
baySeq/man
baySeq/man/CDPost.Rd baySeq/man/CDPriors.Rd baySeq/man/allModels.Rd baySeq/man/baySeq-classes.Rd baySeq/man/baySeq-package.Rd baySeq/man/bimodalSep.Rd baySeq/man/densityFunction.Rd baySeq/man/densityFunctions.Rd baySeq/man/getLibsizes.Rd baySeq/man/getLikelihoods.Rd baySeq/man/getPosteriors.Rd baySeq/man/getPriors.Rd baySeq/man/getTPs.Rd baySeq/man/makeOrderings.Rd baySeq/man/marginaliseEqual.Rd baySeq/man/marginalisePairwise.Rd baySeq/man/methObservables.Rd baySeq/man/mobAnnotation.Rd baySeq/man/mobData.Rd baySeq/man/pairData.Rd baySeq/man/plotMA.CD.Rd baySeq/man/plotNullPrior.Rd baySeq/man/plotPosteriors.Rd baySeq/man/plotPriors.Rd baySeq/man/selectTop.Rd baySeq/man/simData.Rd baySeq/man/summarisePosteriors.Rd baySeq/man/topCounts.Rd baySeq/man/zimData.Rd
baySeq/vignettes
baySeq/vignettes/baySeq.Rnw
baySeq/vignettes/baySeq_generic.Rnw
baySeq/vignettes/priorlog.txt

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