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

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

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