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epigenomix (version 1.12.0)

Epigenetic and gene transcription data normalization and integration with mixture models

Description

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.

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Version

Version

1.12.0

License

LGPL-3

Maintainer

HansUlrich Klein

Last Published

February 15th, 2017

Functions in epigenomix (1.12.0)

mappedReads

Mapped reads obtained from a anti-histone ChIP-seq experiment.
fpkm

Example RNA-seq data set.
plotClassification

Plot classification obtained from a mixture model.
MixModel-class

Class "MixModel"
calculateCrossCorrelation

Calculate the cross correlation for a given GRanges object.
normalizeChIP

Normalization of ChIP-seq count data. (deprecated)
MixModelML-class

Class "MixModelML"
summarizeReads

Count reads lying within given regions.
bayesMixModel

Fits a Bayesian mixture model using Markov Chain Monte Carlo (MCMC) methods
integrateData

Calculates a normalized correlation score from ChIP-seq and microarray gene expression data.
plotComponents

Plots the mixture density together with the densities of all single components.
matchProbeToPromoter

A function assigning promoter regions to given probe IDs.
transToTSS

A data frame with Ensemble transcript IDs and transcriptional start sites.
plotChains

Produces trace plots for a Bayesian mixture model
MixModelBayes-class

Class "MixModelBayes"
eSet

Example gene expression data set.
mlMixModel

Fits a mixture model using the maximum likelihood principle.
ChIPseqSet-class

Class "ChIPseqSet"
MixtureComponent-class

Class "MixtureComponent"
getAlignmentQuality

Calculation of basic alignments statistics
normalize

Normalization of ChIP-seq and other count data