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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("epigenomix")
AuthorHans-Ulrich Klein, Martin Schaefer
Bioconductor views ChIPSeq Classification DifferentialExpression GeneExpression
Date of publicationNone
MaintainerHans-Ulrich Klein <h.klein@uni-muenster.de>
LicenseLGPL-3
Version1.16.0

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

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

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

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