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A B C D E G H L M N P R S T W misc
| ChIPseqR-package | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| $,ReadCounts,ANY-method | Class "ReadCounts" |
| $<-,ReadCounts,ANY,ANY-method | Class "ReadCounts" |
| $<-,ReadCounts-method | Class "ReadCounts" |
| alignFeature | Read counts relative to annotated features |
| as.data.frame,BindScore-method | Class "BindScore" |
| binding | Access slots of S4 classes |
| binding,ANY-method | Access slots of S4 classes |
| binding,BindScore-method | Class "BindScore" |
| binding-methods | Access slots of S4 classes |
| BindScore | Class "BindScore" |
| BindScore-class | Class "BindScore" |
| callBindingSites | Predict protein binding sites from high-throughput sequencing data |
| callBindingSites,ANY-method | Predict protein binding sites from high-throughput sequencing data |
| callBindingSites,character-method | Predict protein binding sites from high-throughput sequencing data |
| callBindingSites,matrix-method | Predict protein binding sites from high-throughput sequencing data |
| callBindingSites,ReadCounts-method | Predict protein binding sites from high-throughput sequencing data |
| callBindingSites-methods | Predict protein binding sites from high-throughput sequencing data |
| ChIPseqR | Identifying Protein Binding Sites in High-Throughput Sequencing Data |
| chrLength | Class "ReadCounts" |
| chrLength,BindScore-method | Class "BindScore" |
| chrLength,ReadCounts-method | Class "ReadCounts" |
| chrLength,RLEReadCounts-method | Run-length Encoded Read Counts |
| compress | Methods for Function compress in Package 'ChIPseqR' |
| compress,BindScore-method | Compress BindScore Objects |
| compress,ReadCounts-method | Compress ReadCount Objects |
| compress,RLEBindScore-method | Methods for Function compress in Package 'ChIPseqR' |
| compress,RLEReadCounts-method | Methods for Function compress in Package 'ChIPseqR' |
| compress-BindScore | Compress BindScore Objects |
| compress-methods | Methods for Function compress in Package 'ChIPseqR' |
| cutoff | Access slots of S4 classes |
| cutoff,ANY-method | Access slots of S4 classes |
| cutoff,BindScore-method | Class "BindScore" |
| cutoff-methods | Access slots of S4 classes |
| cutoff<- | Access slots of S4 classes |
| cutoff<-,ANY-method | Access slots of S4 classes |
| cutoff<-,BindScore-method | Class "BindScore" |
| cutoff<--methods | Access slots of S4 classes |
| decompress | Extract Read Count and Binding Site Score Representations |
| decompress,ANY-method | Methods for Function decompress in Package 'ChIPseqR' |
| decompress,Rle-method | Methods for Function decompress in Package 'ChIPseqR' |
| decompress,RLEBindScore-method | Extract Read Count and Binding Site Score Representations |
| decompress,RleList-method | Methods for Function decompress in Package 'ChIPseqR' |
| decompress,RLEReadCounts-method | Extract Read Count and Binding Site Score Representations |
| decompress-methods | Methods for Function decompress in Package 'ChIPseqR' |
| exportBindSequence | Export sequence of predicted binding sites |
| getBindCor | Calculate cross-correlation between read counts |
| getBindLen | Estimate length of binding and support region |
| getCutoff | Determine significance threshold for binding site scores |
| head,BindScore-method | Class "BindScore" |
| lapply,BindScore-method | Class "BindScore" |
| lapply,ReadCounts-method | Class "ReadCounts" |
| length,BindScore-method | Class "BindScore" |
| length,ReadCounts-method | Class "ReadCounts" |
| length<-,BindScore-method | Class "BindScore" |
| length<-,ReadCounts-method | Class "ReadCounts" |
| max,BindScore-method | Class "BindScore" |
| min,BindScore-method | Class "BindScore" |
| names,BindScore-method | Class "BindScore" |
| names,ReadCounts-method | Class "ReadCounts" |
| names<-,BindScore,ANY-method | Class "BindScore" |
| names<-,ReadCounts,ANY-method | Class "ReadCounts" |
| nreads | Class "ReadCounts" |
| nreads,ReadCounts-method | Class "ReadCounts" |
| nreads,RLEReadCounts-method | Run-length Encoded Read Counts |
| nullDist | Access slots of S4 classes |
| nullDist,ANY-method | Access slots of S4 classes |
| nullDist,BindScore-method | Class "BindScore" |
| nullDist-methods | Access slots of S4 classes |
| nullDist<- | Access slots of S4 classes |
| nullDist<-,ANY-method | Access slots of S4 classes |
| nullDist<-,BindScore-method | Class "BindScore" |
| nullDist<--methods | Access slots of S4 classes |
| peaks | Access slots of S4 classes |
| peaks,ANY-method | Access slots of S4 classes |
| peaks,BindScore-method | Class "BindScore" |
| peaks-methods | Access slots of S4 classes |
| pickPeak | Identify peaks above a given threshold |
| plot,BindScore,missing-method | Diagnostic Plots for Binding Site Scores |
| plot,ReadCounts,missing-method | Diagnostic Plots for Read Counts |
| plot,RLEReadCounts,missing-method | Diagnostic Plots for Read Counts |
| pos2gff | Convert genome coordinates into GFF format |
| pvalue | Access slots of S4 classes |
| pvalue,ANY-method | Access slots of S4 classes |
| pvalue-methods | Access slots of S4 classes |
| range,BindScore-method | Class "BindScore" |
| ReadCounts | Class "ReadCounts" |
| ReadCounts-class | Class "ReadCounts" |
| RLEBindScore-class | Run-length Encoded Binding Site Scores |
| RLEReadCounts-class | Run-length Encoded Read Counts |
| sapply,ReadCounts-method | Class "ReadCounts" |
| score | Access slots of S4 classes |
| score,BindScore-method | Class "BindScore" |
| simpleNucCall | Predict nucleosome positions from high-throughput sequencing data |
| startScore | Score potential protein binding sites |
| strandPileup | Strand specific read counts |
| strandPileup,AlignedRead-method | Strand specific read counts |
| strandPileup,data.frame-method | Strand specific read counts |
| strandPileup-methods | Strand specific read counts |
| support | Access slots of S4 classes |
| support,ANY-method | Access slots of S4 classes |
| support,BindScore-method | Class "BindScore" |
| support-methods | Access slots of S4 classes |
| tail,BindScore-method | Class "BindScore" |
| windowCounts | Summarize read counts in a sliding window |
| [,BindScore,ANY,missing,missing-method | Class "BindScore" |
| [,ReadCounts,ANY,missing,missing-method | Class "ReadCounts" |
| [<-,ReadCounts,ANY,missing-method | Class "ReadCounts" |
| [[,BindScore,ANY,missing-method | Class "BindScore" |
| [[,BindScore,ANY,numeric-method | Class "BindScore" |
| [[,ReadCounts,ANY,missing-method | Class "ReadCounts" |
| [[<-,ReadCounts,ANY,missing-method | Class "ReadCounts" |