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 <firstname.lastname@example.org>|
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...