nucleR: Nucleosome positioning package for R
Version 2.8.0

Nucleosome positioning for Tiling Arrays and NGS experiments.

Browse man pages Browse package API and functions Browse package files

AuthorOscar Flores, Ricard Illa
Bioconductor views ChIPSeq Genetics Microarray Sequencing
Date of publicationNone
MaintainerRicard Illa <ricard.illa@irbbarcelona.org>
LicenseLGPL (>= 3)
Version2.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("nucleR")

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...
readBAM: Import reads from a list of BAM files.
syntheticNucMap: Generates a synthetic nucleosome map

Functions

.export.bed Man page
bamFlagMatrix Source code
buildGRSingle Source code
buildReadsPaired Source code
check.mc Source code
checkConsistency Source code
controlCorrection Man page
controlCorrection,Rle-method Man page
controlCorrection,SimpleRleList-method Man page
controlCorrection,list-method Man page
controlCorrection,numeric-method Man page
coverAround Source code
coverAroundDF Source code
coverAroundIR Source code
coverAroundSC1 Source code
coverAround_1cor Source code
coverage.rpm Man page Source code
doPlot Source code
export.bed Man page Source code
export.bed,CompressedIRangesList-method Man page
export.bed,GRanges-method Man page
export.bed,IRanges-method Man page
export.bed,RangedData-method Man page
export.wig Man page Source code
filterFFT Man page Source code
filterFFT,Rle-method Man page
filterFFT,SimpleRleList-method Man page
filterFFT,list-method Man page
filterFFT,numeric-method Man page
filterNAs Source code
fragmentLenDetect Man page
fragmentLenDetect,AlignedRead-method Man page
fragmentLenDetect,RangedData-method Man page
getPos Source code
mergeCalls Man page Source code
mergeSpace Source code
mid Source code
nt2base Source code
nucleR Man page
nucleR-package Man page
nucleosomePatterns Source code
nucleosomePatternsDF Source code
nucleosome_htseq Man page
nucleosome_tiling Man page
pcKeepCompDetect Man page Source code
peakDetection Man page
peakDetection,list-method Man page
peakDetection,numeric-method Man page
peakScoring Man page
peakScoring,IRanges-method Man page
peakScoring,IRangesList-method Man page
peakScoring,list-method Man page
peakScoring,numeric-method Man page
plotCoverIndiv Source code
plotCoverOverlap Source code
plotPatterns Source code
plotPeaks Man page
plotPeaks,IRanges-method Man page
plotPeaks,RangedData-method Man page
plotPeaks,data.frame-method Man page
plotPeaks,numeric-method Man page
processPairedEnd Source code
processReads Man page
processReads,AlignedRead-method Man page
processReads,RangedData-method Man page
processSingleEnd Source code
processStrand Source code
processTilingArray Man page Source code
readAlignedBatch Source code
readBAM Man page Source code
readBamFile Source code
readSingleFile Source code
removeRepeated Source code
sampleData Source code
syntheticNucMap Man page Source code
xlapply Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/TODO
R/TODO/importBowtie.R
R/TODO/nucleoCluster-methods.R
R/TODO/plotCoverOverlap.R
R/controlCorrection-methods.R
R/coverage.rpm.R
R/export.bed-methods.R
R/export.wig.R
R/filterFFT-methods.R
R/fragmentLenDetect-methods.R
R/importBAM.R
R/mergeCalls.R
R/pcKeepCompDetect.R
R/peakDetection-methods.R
R/peakScoring-methods.R
R/plotPeaks.R
R/processReads-methods.R
R/processTilingArray.R
R/syntheticNucMap.R
README
build
build/vignette.rds
data
data/nucleosome_htseq.rda
data/nucleosome_tiling.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/nucleR.R
inst/doc/nucleR.Rnw
inst/doc/nucleR.pdf
man
man/controlCorrection.Rd
man/coverage.rpm.Rd
man/export.bed.Rd
man/export.wig.Rd
man/filterFFT.Rd
man/fragmentLenDetect.Rd
man/mergeCalls.Rd
man/nucleR-package.Rd
man/nucleosome_htseq.Rd
man/nucleosome_tiling.Rd
man/pcKeepCompDetect.Rd
man/peakDetection.Rd
man/peakScoring.Rd
man/plotPeaks.Rd
man/processReads.Rd
man/processTilingArray.Rd
man/readBAM.rd
man/syntheticNucMap.Rd
vignettes
vignettes/nucleR.Rnw
vignettes/references.bib
nucleR documentation built on May 20, 2017, 10:44 p.m.