Package: nucleR 2.39.0

Alba Sala

nucleR: Nucleosome positioning package for R

Nucleosome positioning for Tiling Arrays and NGS experiments.

Authors:Oscar Flores, Ricard Illa

nucleR_2.39.0.tar.gz
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nucleR.pdf |nucleR.html✨
nucleR/json (API)
NEWS

# Install 'nucleR' in R:
install.packages('nucleR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • nucleosome_htseq - Example reads from high-troughtput sequencing nucleosome positioning experiment
  • nucleosome_tiling - Example intensities from Tiling Microarray nucleosome positioning experiment

On BioConductor:nucleR-2.37.0(bioc 3.20)nucleR-2.36.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

nucleosomepositioningcoveragechipseqmicroarraysequencinggeneticsqualitycontroldataimport

5.32 score 21 scripts 285 downloads 10 mentions 16 exports 80 dependencies

Last updated 23 days agofrom:242e3bb478. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 31 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 31 2024
R-4.4-macWARNINGOct 31 2024
R-4.3-winWARNINGOct 31 2024
R-4.3-macWARNINGOct 31 2024

Exports:controlCorrectioncoverage.rpmexport.bedexport.wigfilterFFTfragmentLenDetectmergeCallspcKeepCompDetectpeakDetectionpeakScoringplotPeaksprocessReadsprocessTilingArrayreadBAMreadBowtiesyntheticNucMap

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopsclicodetoolscolorspacecpp11crayoncurlDelayedArraydeldirdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrhwriterinterpIRangesisobandjpegjsonlitelabelinglambda.rlatticelatticeExtralifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpngpwalignR6RColorBrewerRcppRcppEigenRhtslibrlangRsamtoolsS4ArraysS4VectorsscalesShortReadsnowSparseArraySummarizedExperimentsystibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Quick analysis of nucleosome positioning experiments using the nucleR package

Oscar Flores Guri

Rendered fromnucleR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2020-11-14
Started: 2018-02-07

Readme and manuals

Help Manual

Help pageTopics
Nucleosome positioning package for RnucleR-package nucleR
FFT Region.fftRegion
Threshold getter.getThreshold
File loader Higher order function to import BAM or Bowtie files. Deals with wether type is 'single' or 'paired' and with the number of input files.loadFiles
Load a paired-end-end BAM.loadPairedBam
Load a single-end BAM.loadSingleBam
Find midpoints.mid
Process a given strand from a BAM file to read.processStrand
Unlist an IRanges object into a vector.unlist_as_integer
Vectorized version of 'all'.vectorizedAll
mclapply warapper.xlapply
Correct experimental profiles with control samplecontrolCorrection controlCorrection,list-method controlCorrection,numeric-method controlCorrection,Rle-method controlCorrection,SimpleRleList-method
Coverage calculation and normalization to reads per million (rpm)coverage.rpm coverage.rpm,CompressedGRangesList-method coverage.rpm,GRanges-method coverage.rpm,IRanges-method
Export ranges in BED formatexport.bed export.bed,CompressedIRangesList-method export.bed,GRanges-method export.bed,IRanges-method
Export values in WIG formatexport.wig
Clean noise and smoothing for genomic data using Fourier-analysisfilterFFT filterFFT,list-method filterFFT,numeric-method filterFFT,Rle-method filterFFT,SimpleRleList-method
Fragments length detection from single-end sequencing samplesfragmentLenDetect fragmentLenDetect,AlignedRead-method fragmentLenDetect,GRanges-method
Automatic merging of overlapped nucleosome callsmergeCalls mergeCalls,GRanges-method
Example reads from high-troughtput sequencing nucleosome positioning experimentnucleosome_htseq
Example intensities from Tiling Microarray nucleosome positioning experimentnucleosome_tiling
Auto detection of a fitted 'pcKeepComp' param for filterFFT functionpcKeepCompDetect
Detect peaks (local maximum) from values seriespeakDetection peakDetection,list-method peakDetection,numeric-method
Peak scoring functionpeakScoring peakScoring,IRanges-method peakScoring,IRangesList-method peakScoring,list-method peakScoring,numeric-method
Nucleosome calling plot functionplotPeaks plotPeaks,data.frame-method plotPeaks,GRanges-method plotPeaks,IRanges-method plotPeaks,numeric-method
Process reads from High-Troughtput Sequencing experimentsprocessReads processReads,AlignedRead-method processReads,CompressedGRangesList-method processReads,GRanges-method
Obtain and clean nucleosome positioning data from tiling arrayprocessTilingArray
Import reads from a list of BAM files.readBAM
Import reads from a vector of Bowtie filesreadBowtie
Generates a synthetic nucleosome mapsyntheticNucMap