nucleR: Nucleosome positioning package for R

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Nucleosome positioning for Tiling Arrays and NGS experiments.

Author
Oscar Flores, Ricard Illa
Date of publication
None
Maintainer
Ricard Illa <ricard.illa@irbbarcelona.org>
License
LGPL (>= 3)
Version
2.6.0

View on Bioconductor

Man pages

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

Files in this package

nucleR/DESCRIPTION
nucleR/NAMESPACE
nucleR/R
nucleR/R/AllGenerics.R
nucleR/R/TODO
nucleR/R/TODO/importBowtie.R
nucleR/R/TODO/nucleoCluster-methods.R
nucleR/R/TODO/plotCoverOverlap.R
nucleR/R/controlCorrection-methods.R
nucleR/R/coverage.rpm.R
nucleR/R/export.bed-methods.R
nucleR/R/export.wig.R
nucleR/R/filterFFT-methods.R
nucleR/R/fragmentLenDetect-methods.R
nucleR/R/importBAM.R
nucleR/R/mergeCalls.R
nucleR/R/pcKeepCompDetect.R
nucleR/R/peakDetection-methods.R
nucleR/R/peakScoring-methods.R
nucleR/R/plotPeaks.R
nucleR/R/processReads-methods.R
nucleR/R/processTilingArray.R
nucleR/R/syntheticNucMap.R
nucleR/README
nucleR/build
nucleR/build/vignette.rds
nucleR/data
nucleR/data/nucleosome_htseq.rda
nucleR/data/nucleosome_tiling.rda
nucleR/inst
nucleR/inst/CITATION
nucleR/inst/NEWS
nucleR/inst/doc
nucleR/inst/doc/nucleR.R
nucleR/inst/doc/nucleR.Rnw
nucleR/inst/doc/nucleR.pdf
nucleR/man
nucleR/man/controlCorrection.Rd
nucleR/man/coverage.rpm.Rd
nucleR/man/export.bed.Rd
nucleR/man/export.wig.Rd
nucleR/man/filterFFT.Rd
nucleR/man/fragmentLenDetect.Rd
nucleR/man/mergeCalls.Rd
nucleR/man/nucleR-package.Rd
nucleR/man/nucleosome_htseq.Rd
nucleR/man/nucleosome_tiling.Rd
nucleR/man/pcKeepCompDetect.Rd
nucleR/man/peakDetection.Rd
nucleR/man/peakScoring.Rd
nucleR/man/plotPeaks.Rd
nucleR/man/processReads.Rd
nucleR/man/processTilingArray.Rd
nucleR/man/readBAM.rd
nucleR/man/syntheticNucMap.Rd
nucleR/vignettes
nucleR/vignettes/nucleR.Rnw
nucleR/vignettes/references.bib