epigenomix: Epigenetic and gene transcription data normalization and integration with mixture models

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A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.

Author
Hans-Ulrich Klein, Martin Schaefer
Date of publication
None
Maintainer
Hans-Ulrich Klein <h.klein@uni-muenster.de>
License
LGPL-3
Version
1.14.0

View on Bioconductor

Man pages

bayesMixModel
Fits a Bayesian mixture model using Markov Chain Monte Carlo...
calculateCrossCorrelation
Calculate the cross correlation for a given GRanges object.
ChIPseqSet-class
Class '"ChIPseqSet"'
eSet
Example gene expression data set.
fpkm
Example RNA-seq data set.
getAlignmentQuality
Calculation of basic alignments statistics
integrateData
Calculates a normalized correlation score from ChIP-seq and...
mappedReads
Mapped reads obtained from a anti-histone ChIP-seq...
matchProbeToPromoter
A function assigning promoter regions to given probe IDs.
MixModelBayes-class
Class '"MixModelBayes"'
MixModel-class
Class '"MixModel"'
MixModelML-class
Class '"MixModelML"'
MixtureComponent-class
Class '"MixtureComponent"'
mlMixModel
Fits a mixture model using the maximum likelihood principle.
normalize
Normalization of ChIP-seq and other count data
normalizeChIP
Normalization of ChIP-seq count data. (deprecated)
plotChains
Produces trace plots for a Bayesian mixture model
plotClassification
Plot classification obtained from a mixture model.
plotComponents
Plots the mixture density together with the densities of all...
summarizeReads
Count reads lying within given regions.
transToTSS
A data frame with Ensemble transcript IDs and transcriptional...

Files in this package

epigenomix/DESCRIPTION
epigenomix/NAMESPACE
epigenomix/R
epigenomix/R/AllClasses.R
epigenomix/R/AllGenerics.R
epigenomix/R/bayesMixModel.R
epigenomix/R/calculateCrossCorrelation.R
epigenomix/R/getAlignmentQuality.R
epigenomix/R/integrateData.R
epigenomix/R/matchProbeToPromoter.R
epigenomix/R/methods-ChIPseqSet.R
epigenomix/R/methods-MixModel.R
epigenomix/R/methods-MixtureComponent.R
epigenomix/R/mlMixModel.R
epigenomix/R/normalize.R
epigenomix/R/normalizeChIP.R
epigenomix/R/plotChains.R
epigenomix/R/plotClassification.R
epigenomix/R/plotComponents.R
epigenomix/R/summarizeReads.R
epigenomix/build
epigenomix/build/vignette.rds
epigenomix/data
epigenomix/data/eSet.RData
epigenomix/data/fpkm.RData
epigenomix/data/mappedReads.RData
epigenomix/data/transToTSS.RData
epigenomix/inst
epigenomix/inst/CITATION
epigenomix/inst/doc
epigenomix/inst/doc/epigenomix.R
epigenomix/inst/doc/epigenomix.Rnw
epigenomix/inst/doc/epigenomix.pdf
epigenomix/man
epigenomix/man/ChIPseqSet-class.Rd
epigenomix/man/MixModel-class.Rd
epigenomix/man/MixModelBayes-class.Rd
epigenomix/man/MixModelML-class.Rd
epigenomix/man/MixtureComponent-class.Rd
epigenomix/man/bayesMixModel.Rd
epigenomix/man/calculateCrossCorrelation.Rd
epigenomix/man/eSet.Rd
epigenomix/man/fpkm.Rd
epigenomix/man/getAlignmentQuality.Rd
epigenomix/man/integrateData.Rd
epigenomix/man/mappedReads.Rd
epigenomix/man/matchProbeToPromoter.Rd
epigenomix/man/mlMixModel.Rd
epigenomix/man/normalize.Rd
epigenomix/man/normalizeChIP.Rd
epigenomix/man/plotChains.Rd
epigenomix/man/plotClassification.Rd
epigenomix/man/plotComponents.Rd
epigenomix/man/summarizeReads.Rd
epigenomix/man/transToTSS.Rd
epigenomix/vignettes
epigenomix/vignettes/epigenomix.Rnw
epigenomix/vignettes/epigenomix.bib
epigenomix/vignettes/unsrturl.bst