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nucleR (version 2.4.0)

Nucleosome positioning package for R

Description

Nucleosome positioning for Tiling Arrays and NGS experiments.

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Version

Version

2.4.0

License

LGPL (>= 3)

Maintainer

Ricard Illa

Last Published

February 15th, 2017

Functions in nucleR (2.4.0)

processReads

Process reads from High-Troughtput Sequencing experiments
controlCorrection

Correct experimental profiles with control sample
fragmentLenDetect

Fragments length detection from single-end sequencing samples
peakDetection

Detect peaks (local maximum) from values series
processTilingArray

Obtain and clean nucleosome positioning data from tiling array
export.wig

Export values in WIG format
nucleosome_htseq

Example reads from high-troughtput sequencing nucleosome positioning experiment
mergeCalls

Automatic merging of overlapped nucleosome calls
plotPeaks

Nucleosome calling plot function
nucleR-package

Nucleosome positioning package for R
coverage.rpm

Coverage calculation and normalization to reads per million (rpm)
nucleosome_tiling

Example intensities from Tiling Microarray nucleosome positioning experiment
filterFFT

Clean noise and smoothing for genomic data using Fourier-analysis
peakScoring

Peak scoring function
export.bed

Export ranges in BED format
readBAM

Import reads from a list of BAM files.
syntheticNucMap

Generates a synthetic nucleosome map
pcKeepCompDetect

Auto detection of a fitted pcKeepComp param for filterFFT function