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

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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.

Author
Thomas J. Hardcastle
Date of publication
None
Maintainer
Thomas J. Hardcastle <tjh48@cam.ac.uk>
License
GPL-3
Version
2.8.0

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

Files in this package

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