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

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.

AuthorHans-Ulrich Klein, Martin Schaefer
Date of publicationNone
MaintainerHans-Ulrich Klein <h.klein@uni-muenster.de>
LicenseLGPL-3
Version1.14.0

View on Bioconductor

Functions

acceptanceRate Man page
acceptanceRate,MixModelBayes-method Man page
as.data.frame,MixModel-method Man page
bayesMixModel Man page
bayesMixModel,numeric-method Man page
calculateCrossCorrelation Man page
calculateCrossCorrelation,GRanges-method Man page
chains Man page
chains,MixModelBayes-method Man page
ChIPseqSet Man page
ChIPseqSet-class Man page
ChIPseqSet,matrix,GRangesList-method Man page
ChIPseqSet,matrix,GRanges-method Man page
chipVals Man page
chipVals<- Man page
chipVals<-,ChIPseqSet,matrix-method Man page
chipVals,ChIPseqSet-method Man page
classification Man page
classification,MixModel,character-method Man page
classification,MixModel,missing-method Man page
components Man page
components,MixModel-method Man page
convergence Man page
convergence,MixModelML-method Man page
cpm Man page
cpm,ChIPseqSet-method Man page
dim,MixModel-method Man page
eSet Man page
fpkm Man page
getAlignmentQuality Man page
getAlignmentQuality,character-method Man page
integrateData Man page
integrateData,ExpressionSet,ChIPseqSet,character,character-metho Man page
integrateData,ExpressionSet,ChIPseqSet,character,missing-method Man page
integrateData,ExpressionSetIllumina,ChIPseqSet,character,charact Man page
integrateData,ExpressionSetIllumina,ChIPseqSet,character,missing Man page
length,MixModel-method Man page
listClassificationMethods Man page
listClassificationMethods,MixModel-method Man page
mappedReads Man page
matchProbeToPromoter Man page
matchProbeToPromoter,list,data.frame-method Man page
MixModelBayes-class Man page
MixModel-class Man page
MixModelML-class Man page
MixtureComponent-class Man page
mlMixModel Man page
mlMixModel,numeric-method Man page
mmData Man page
mmData,MixModel-method Man page
normalize Man page
normalizeChIP Man page
normalizeChIP,ChIPseqSet,character-method Man page
normalize,ChIPseqSet-method Man page
normalize,ExpressionSet-method Man page
plotChains Man page
plotChains,MixModelBayes-method Man page
plotClassification Man page
plotClassification,MixModel-method Man page
plotComponents Man page
plotComponents,MixModel-method Man page
show,MixModel-method Man page
show,MixtureComponent-method Man page
summarizeReads Man page
summarizeReads,GRangesList,GRanges,character-method Man page
summarizeReads,GRangesList,GRangesList,character-method Man page
summarizeReads,GRangesList,GRangesList,missing-method Man page
summarizeReads,GRangesList,GRanges,missing-method Man page
summary,MixModelBayes-method Man page
summary,MixModel-method Man page
transToTSS Man page
weights,MixModel-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.