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:
ChIPseqR_1.67.0.tar.gz
ChIPseqR_1.67.0.zip(r-4.7)ChIPseqR_1.67.0.zip(r-4.6)ChIPseqR_1.67.0.zip(r-4.5)
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)
ChIPseqR_1.67.0.tar.gz(r-4.7-arm64)ChIPseqR_1.67.0.tar.gz(r-4.7-x86_64)ChIPseqR_1.67.0.tar.gz(r-4.6-arm64)ChIPseqR_1.67.0.tar.gz(r-4.6-x86_64)
ChIPseqR_1.67.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
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.
Last updated from:2ef23a492a. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 192 | ||
| linux-devel-arm64 | NOTE | 296 | ||
| linux-devel-x86_64 | NOTE | 381 | ||
| source / vignettes | OK | 267 | ||
| linux-release-arm64 | NOTE | 288 | ||
| linux-release-x86_64 | NOTE | 350 | ||
| macos-release-arm64 | NOTE | 183 | ||
| macos-release-x86_64 | NOTE | 478 | ||
| macos-oldrel-arm64 | NOTE | 203 | ||
| macos-oldrel-x86_64 | NOTE | 333 | ||
| windows-devel | NOTE | 320 | ||
| windows-release | NOTE | 305 | ||
| windows-oldrel | NOTE | 422 | ||
| wasm-release | OK | 130 |
Exports:alignFeatureallGroupsallWordsas.data.framebindingBindScorecallBindingSiteschrLengthcompresscutoffcutoff<-decompressdiNucTestexportBindSequencegetBindCorgetBindLengetCutoffheadlapplynreadsnullDistnullDist<-oligoNucTestpeakspickPeakplotplotFreqpos2gffpvalueReadCountssapplyscoresimpleNucCallstartScorestrandPileupsupporttailtriNucTest1triNucTest2views2nucFreqwindowCounts
Dependencies:abindBHBiobaseBiocGenericsBiocParallelBiostringsbitopscigarillocodetoolscpp11crayonDelayedArraydeldirfBasicsformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgssHilbertVishwriterinterpIRangesjpeglambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatspngpwalignRColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsSeqinfoShortReadsnowSparseArrayspatialstabledistSummarizedExperimenttimeDatetimeSeriestimsacXVector
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 |
