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

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

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