Man pages for epigenomix
Epigenetic and gene transcription data normalization and integration with mixture models
| 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... |
