Package: ChIPseqR 1.67.0

Peter Humburg

ChIPseqR: Identifying Protein Binding Sites in High-Throughput Sequencing Data

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

Authors:Peter Humburg

ChIPseqR_1.67.0.tar.gz
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ChIPseqR_1.67.0.tgz(r-4.6-x86_64)ChIPseqR_1.67.0.tgz(r-4.6-arm64)ChIPseqR_1.67.0.tgz(r-4.5-x86_64)ChIPseqR_1.67.0.tgz(r-4.5-arm64)
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ChIPseqR_1.67.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ChIPseqR/json (API)

# Install 'ChIPseqR' in R:

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

On BioConductor:ChIPseqR-1.67.0(bioc 3.24)ChIPseqR-1.66.0(bioc 3.23)

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

chipseq infrastructure

4.70 score 2 scripts 518 downloads 5 mentions 41 exports 53 dependencies

Last updated from:2ef23a492a. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	208
linux-devel-arm64	NOTE	349
linux-devel-x86_64	NOTE	531
source / vignettes	OK	351
linux-release-arm64	NOTE	327
linux-release-x86_64	NOTE	399
macos-release-arm64	NOTE	190
macos-release-x86_64	NOTE	492
macos-oldrel-arm64	NOTE	214
macos-oldrel-x86_64	NOTE	696
windows-devel	NOTE	322
windows-release	NOTE	310
windows-oldrel	NOTE	400
wasm-release	OK	159

Exports:alignFeature allGroups allWords as.data.frame binding BindScore callBindingSites chrLength compress cutoff cutoff<-decompress diNucTest exportBindSequence getBindCor getBindLen getCutoff head lapply nreads nullDist nullDist<-oligoNucTest peaks pickPeak plot plotFreq pos2gff pvalue ReadCounts sapply score simpleNucCall startScore strandPileup support tail triNucTest1 triNucTest2 views2nucFreq windowCounts

Dependencies:abind BH Biobase BiocGenerics BiocParallel Biostrings bitops cigarillo codetools cpp11 crayon DelayedArray deldir fBasics formatR futile.logger futile.options generics GenomicAlignments GenomicRanges gss HilbertVis hwriter interp IRanges jpeg lambda.r lattice latticeExtra MASS Matrix MatrixGenerics matrixStats png pwalign RColorBrewer Rcpp RcppEigen Rhtslib Rsamtools S4Arrays S4Vectors Seqinfo ShortRead snow SparseArray spatial stabledist SummarizedExperiment timeDate timeSeries timsac XVector

Introduction to ChIPseqR

Rendered fromIntroduction.Rnwusingutils::Sweave

Last update: 2015-03-11
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Identifying Protein Binding Sites in High-Throughput Sequencing Data	ChIPseqR-package ChIPseqR
Access slots of S4 classes	binding binding,ANY-method binding-methods cutoff cutoff,ANY-method cutoff-methods cutoff<- cutoff<-,ANY-method cutoff<--methods nullDist nullDist,ANY-method nullDist-methods nullDist<- nullDist<-,ANY-method nullDist<--methods peaks peaks,ANY-method peaks-methods pvalue pvalue,ANY-method pvalue-methods score support support,ANY-method support-methods
Read counts relative to annotated features	alignFeature
Class "BindScore"	as.data.frame,BindScore-method binding,BindScore-method BindScore BindScore-class chrLength,BindScore-method cutoff,BindScore-method cutoff<-,BindScore-method head,BindScore-method lapply,BindScore-method length,BindScore-method length<-,BindScore-method max,BindScore-method min,BindScore-method names,BindScore-method names<-,BindScore,ANY-method nullDist,BindScore-method nullDist<-,BindScore-method peaks,BindScore-method range,BindScore-method score,BindScore-method support,BindScore-method tail,BindScore-method [,BindScore,ANY,missing,missing-method [[,BindScore,ANY,missing-method [[,BindScore,ANY,numeric-method
Predict protein binding sites from high-throughput sequencing data	callBindingSites callBindingSites,ANY-method callBindingSites,character-method callBindingSites,matrix-method callBindingSites,ReadCounts-method callBindingSites-methods
Compress BindScore Objects	compress,BindScore-method compress-BindScore
Methods for Function compress in Package `ChIPseqR'	compress compress,RLEBindScore-method compress,RLEReadCounts-method compress-methods
Compress ReadCount Objects	compress,ReadCounts-method
Extract Read Count and Binding Site Score Representations	decompress decompress,RLEBindScore-method decompress,RLEReadCounts-method
Methods for Function decompress in Package `ChIPseqR'	decompress,ANY-method decompress,Rle-method decompress,RleList-method decompress-methods
Export sequence of predicted binding sites	exportBindSequence
Calculate cross-correlation between read counts	getBindCor
Estimate length of binding and support region	getBindLen
Determine significance threshold for binding site scores	getCutoff
Identify peaks above a given threshold	pickPeak
Diagnostic Plots for Binding Site Scores	plot,BindScore,missing-method
Diagnostic Plots for Read Counts	plot,ReadCounts,missing-method plot,RLEReadCounts,missing-method
Convert genome coordinates into GFF format	pos2gff
Class "ReadCounts"	$,ReadCounts-method $<-,ReadCounts,ANY-method $<-,ReadCounts-method chrLength chrLength,ReadCounts-method lapply,ReadCounts-method length,ReadCounts-method length<-,ReadCounts-method names,ReadCounts-method names<-,ReadCounts,ANY-method nreads nreads,ReadCounts-method ReadCounts ReadCounts-class sapply,ReadCounts-method [,ReadCounts,ANY,missing,missing-method [<-,ReadCounts,ANY,missing,ANY-method [<-,ReadCounts,ANY,missing-method [[,ReadCounts,ANY,missing-method [[<-,ReadCounts,ANY,missing,ANY-method [[<-,ReadCounts,ANY,missing-method
Run-length Encoded Binding Site Scores	RLEBindScore-class
Run-length Encoded Read Counts	chrLength,RLEReadCounts-method nreads,RLEReadCounts-method RLEReadCounts-class
Predict nucleosome positions from high-throughput sequencing data	simpleNucCall
Score potential protein binding sites	startScore
Strand specific read counts	strandPileup strandPileup,AlignedRead-method strandPileup,data.frame-method strandPileup-methods
Summarize read counts in a sliding window	windowCounts