|controlEM||Control parameters of the EM algorithm from mixNBHMM|
|createOffset||Create Offsets for Peak Calling|
|cutoff||DEPRECATED, USE fdrControl INSTEAD!|
|ENCODE||ChIP-seq read counts of H3K36me3 of GM12878, H1-hESC, and...|
|fdrControl||Classification of genomic windows given an FDR control...|
|hg19.blacklist.v2||Blacklisted genomic regions for functional genomics analysis...|
|mixNBHMM||Three-state HMM with mixture model for differential peak...|
|mixNBHMMDataSetFromBam||Create a mixNBHMMDataSet from a set of BAM files|
|mixZINBHMM||Three-state HMM with mixture model for differential peak...|
|plotPeaks||Create a plot of ChIP read counts with called peaks and...|
|simulateHMM||Simulate a hidden Markov model path (HMM)|
|summarizePeaks||Summarize peak calls and optionally create a BED 6+3 file in...|
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