Package: ChIPseqR 1.61.0
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_1.61.0.tar.gz
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ChIPseqR.pdf |ChIPseqR.html✨
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-1.61.0(bioc 3.21)ChIPseqR-1.60.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 19 days agofrom:87a6195288. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:alignFeatureallGroupsallWordsas.data.framebindingBindScorecallBindingSiteschrLengthcompresscutoffcutoff<-decompressdiNucTestexportBindSequencegetBindCorgetBindLengetCutoffheadlapplynreadsnullDistnullDist<-oligoNucTestpeakspickPeakplotplotFreqpos2gffpvalueReadCountssapplyscoresimpleNucCallstartScorestrandPileupsupporttailtriNucTest1triNucTest2views2nucFreqwindowCounts
Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitopscodetoolscpp11crayoncurlDelayedArraydeldirfBasicsformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesgssHilbertVishttrhwriterinterpIRangesjpegjsonlitelambda.rlatticelatticeExtraMASSMatrixMatrixGenericsmatrixStatsmimeopensslpngpwalignR6RColorBrewerRcppRcppEigenRhtslibRsamtoolsS4ArraysS4VectorsShortReadsnowSparseArrayspatialstabledistSummarizedExperimentsystimeDatetimeSeriestimsacUCSC.utilsXVectorzlibbioc
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 |
