Nucleosome positioning package for R


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Documentation for package ‘nucleR’ version 2.16.0

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nucleR-package Nucleosome positioning package for R
controlCorrection Correct experimental profiles with control sample
controlCorrection-method Correct experimental profiles with control sample
coverage.rpm Coverage calculation and normalization to reads per million (rpm)
coverage.rpm-method Coverage calculation and normalization to reads per million (rpm)
export.bed Export ranges in BED format
export.bed-method Export ranges in BED format
export.wig Export values in WIG format
filterFFT Clean noise and smoothing for genomic data using Fourier-analysis
filterFFT-method Clean noise and smoothing for genomic data using Fourier-analysis
fragmentLenDetect Fragments length detection from single-end sequencing samples
fragmentLenDetect-method Fragments length detection from single-end sequencing samples
mergeCalls Automatic merging of overlapped nucleosome calls
mergeCalls-method Automatic merging of overlapped nucleosome calls
nucleosome_htseq Example reads from high-troughtput sequencing nucleosome positioning experiment
nucleosome_tiling Example intensities from Tiling Microarray nucleosome positioning experiment
nucleR Nucleosome positioning package for R
pcKeepCompDetect Auto detection of a fitted 'pcKeepComp' param for filterFFT function
peakDetection Detect peaks (local maximum) from values series
peakDetection-method Detect peaks (local maximum) from values series
peakScoring Peak scoring function
peakScoring-method Peak scoring function
plotPeaks Nucleosome calling plot function
plotPeaks-method Nucleosome calling plot function
processReads Process reads from High-Troughtput Sequencing experiments
processReads-method Process reads from High-Troughtput Sequencing experiments
processTilingArray Obtain and clean nucleosome positioning data from tiling array
readBAM Import reads from a list of BAM files.
readBowtie Import reads from a vector of Bowtie files
syntheticNucMap Generates a synthetic nucleosome map