dipPeaks: Estimate density and find peaks
In nsheff/dipPeak: A Parzen Density Estimator and Peak Finder

Calculates a smoothed track from input count data, and identifies peaks in the data. Outputs the peaks and smoothed track to file.

dipPeaks(bamFile, bigWigOut = NULL, chromInfo = NULL,
  scratchDirBase = "~", outDir = "~", kernel = "e", cores = 1,
  perChromCutoff = FALSE, windowSize = 50, windowStep = 5,
  indexFile = NULL, retainTemp = FALSE, limitChrom = NULL)

`bamFile`	Input file in bam format
`bigWigOut`	Produce a smoothed output density file in bigwig format (using wigToBigWig)?
`chromInfo`	UCSC chromInfo.txt file (required only for bigWigOut)
`scratchDirBase`	Directory for scratch output; use local disk for optimal processing. dipPeak writes a significant amount of data to disk as it runs, to reduce memory use. This I/O takes time, and will be faster if you use a local disk or fast mount spot.
`outDir`	Final folder (the files to keep will be moved here from the scratch dir).
`kernel`	'e' for Epanechinov; 'g' for Gaussian; 'm' for Mexican Hat
`cores`	Add additional cores (up to 23) for faster processing. (Default:1)
`perChromCutoff`	Boolean; If yes, calculates a per-chromosome; otherwise, defaults to genome-wide cutoff.
`windowSize`	Choose the size of the smoothing window (default:50)
`windowStep`	Choose the window step (5 will take a window every 5 bases) (default:5)
`indexFile`	Index file made from "samtools index" on the bam input file; deaults to bamFile.bai, or you can provide one.
`retainTemp`	Do you want to retain temporary files?
`limitChrom`	You can limit the smoothing to a list of chromosomes (defaults to everything in the bam file)