Package: nucleR 2.45.0

Alba Sala

nucleR: Nucleosome positioning package for R

Nucleosome positioning for Tiling Arrays and NGS experiments.

Authors:Oscar Flores, Ricard Illa

nucleR_2.45.0.tar.gz
nucleR_2.45.0.zip(r-4.7)nucleR_2.45.0.zip(r-4.6)nucleR_2.45.0.zip(r-4.5)
nucleR_2.45.0.tgz(r-4.6-any)nucleR_2.45.0.tgz(r-4.5-any)
nucleR_2.45.0.tar.gz(r-4.7-any)nucleR_2.45.0.tar.gz(r-4.6-any)
nucleR_2.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nucleR/json (API)

# Install 'nucleR' in R:

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

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-2.45.0(bioc 3.24)nucleR-2.44.0(bioc 3.23)

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

nucleosomepositioning coverage chipseq microarray sequencing genetics qualitycontrol dataimport

5.74 score 37 scripts 10 mentions 16 exports 67 dependencies

Last updated from:8456b4012a. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	197
linux-devel-x86_64	WARNING	365
source / vignettes	OK	279
linux-release-x86_64	WARNING	351
macos-release-arm64	WARNING	207
macos-oldrel-arm64	WARNING	285
windows-devel	WARNING	294
windows-release	WARNING	272
windows-oldrel	WARNING	278
wasm-release	OK	172

Exports:controlCorrection coverage.rpm export.bed export.wig filterFFT fragmentLenDetect mergeCalls pcKeepCompDetect peakDetection peakScoring plotPeaks processReads processTilingArray readBAM readBowtie syntheticNucMap

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo cli codetools cpp11 crayon DelayedArray deldir dplyr farver formatR futile.logger futile.options generics GenomicAlignments GenomicRanges ggplot2 glue gtable hwriter interp IRanges isoband jpeg labeling lambda.r lattice latticeExtra lifecycle magrittr MASS Matrix MatrixGenerics matrixStats pillar pkgconfig png pwalign R6 RColorBrewer Rcpp RcppEigen Rhtslib rlang Rsamtools S4Arrays S4Vectors S7 scales Seqinfo ShortRead snow SparseArray SummarizedExperiment tibble tidyselect utf8 vctrs viridisLite withr XVector

Quick analysis of nucleosome positioning experiments using the nucleR package

Rendered fromnucleR.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Nucleosome positioning package for R	nucleR-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 sample	controlCorrection 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 format	export.bed export.bed,CompressedIRangesList-method export.bed,GRanges-method export.bed,IRanges-method
Export values in WIG format	export.wig
Clean noise and smoothing for genomic data using Fourier-analysis	filterFFT filterFFT,list-method filterFFT,numeric-method filterFFT,Rle-method filterFFT,SimpleRleList-method
Fragments length detection from single-end sequencing samples	fragmentLenDetect fragmentLenDetect,AlignedRead-method fragmentLenDetect,GRanges-method
Automatic merging of overlapped nucleosome calls	mergeCalls mergeCalls,GRanges-method
Example reads from high-troughtput sequencing nucleosome positioning experiment	nucleosome_htseq
Example intensities from Tiling Microarray nucleosome positioning experiment	nucleosome_tiling
Auto detection of a fitted 'pcKeepComp' param for filterFFT function	pcKeepCompDetect
Detect peaks (local maximum) from values series	peakDetection peakDetection,list-method peakDetection,numeric-method
Peak scoring function	peakScoring peakScoring,IRanges-method peakScoring,IRangesList-method peakScoring,list-method peakScoring,numeric-method
Nucleosome calling plot function	plotPeaks plotPeaks,data.frame-method plotPeaks,GRanges-method plotPeaks,IRanges-method plotPeaks,numeric-method
Process reads from High-Troughtput Sequencing experiments	processReads processReads,AlignedRead-method processReads,CompressedGRangesList-method processReads,GRanges-method
Obtain and clean nucleosome positioning data from tiling array	processTilingArray
Import reads from a list of BAM files.	readBAM
Import reads from a vector of Bowtie files	readBowtie
Generates a synthetic nucleosome map	syntheticNucMap