| addOffsets | Add offsets to epigraHMMDataSet |
| callPeaks | Summarize peak calls and optionally create a BED 6+3 file in broadPeak format for visualization |
| cleanCounts | Remove effects from covariates of interest |
| controlEM | Control parameters for the EM algorithm from epigraHMM |
| epigraHMM | Perform peak calling of epigenomic data sets |
| epigraHMMDataSetFromBam | Create a epigraHMMDataSet from a set of BAM files |
| epigraHMMDataSetFromMatrix | Create a epigraHMMDataSet from matrices of counts |
| initializer | Initializer of epigraHMM |
| normalizeCounts | Normalize counts |
| plotCounts | Create a plot with the results from epigraHMM |
| plotPatterns | Create a plot of differerential patterns posterior probabilities from epigraHMM |