nucleR-package	nucleR-package
.fftRegion	dot-fftRegion
.getThreshold	dot-getThreshold
.loadFiles	dot-loadFiles
.loadPairedBam	dot-loadPairedBam
.loadSingleBam	dot-loadSingleBam
.mid	dot-mid
.processStrand	dot-processStrand
.unlist_as_integer	dot-unlist_as_integer
.vectorizedAll	dot-vectorizedAll
.xlapply	dot-xlapply
controlCorrection	controlCorrection
controlCorrection,list-method	controlCorrection
controlCorrection,numeric-method	controlCorrection
controlCorrection,Rle-method	controlCorrection
controlCorrection,SimpleRleList-method	controlCorrection
coverage.rpm	coverage.rpm
coverage.rpm,CompressedGRangesList-method	coverage.rpm
coverage.rpm,GRanges-method	coverage.rpm
coverage.rpm,IRanges-method	coverage.rpm
export.bed	export.bed
export.bed,CompressedIRangesList-method	export.bed
export.bed,GRanges-method	export.bed
export.bed,IRanges-method	export.bed
export.wig	export.wig
filterFFT	filterFFT
filterFFT,list-method	filterFFT
filterFFT,numeric-method	filterFFT
filterFFT,Rle-method	filterFFT
filterFFT,SimpleRleList-method	filterFFT
fragmentLenDetect	fragmentLenDetect
fragmentLenDetect,AlignedRead-method	fragmentLenDetect
fragmentLenDetect,GRanges-method	fragmentLenDetect
mergeCalls	mergeCalls
mergeCalls,GRanges-method	mergeCalls
nucleosome_htseq	nucleosome_htseq
nucleosome_tiling	nucleosome_tiling
nucleR	nucleR-package
pcKeepCompDetect	pcKeepCompDetect
peakDetection	peakDetection
peakDetection,list-method	peakDetection
peakDetection,numeric-method	peakDetection
peakScoring	peakScoring
peakScoring,IRanges-method	peakScoring
peakScoring,IRangesList-method	peakScoring
peakScoring,list-method	peakScoring
peakScoring,numeric-method	peakScoring
plotPeaks	plotPeaks
plotPeaks,data.frame-method	plotPeaks
plotPeaks,GRanges-method	plotPeaks
plotPeaks,IRanges-method	plotPeaks
plotPeaks,numeric-method	plotPeaks
processReads	processReads
processReads,AlignedRead-method	processReads
processReads,CompressedGRangesList-method	processReads
processReads,GRanges-method	processReads
processTilingArray	processTilingArray
readBAM	readBAM
readBowtie	readBowtie
syntheticNucMap	syntheticNucMap
