Man pages for ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data
| accessors | Access slots of S4 classes |
| alignFeature | Read counts relative to annotated features |
| BindScore | Class "BindScore" |
| callBindingSites | Predict protein binding sites from high-throughput sequencing... |
| ChIPseqR-package | Identifying Protein Binding Sites in High-Throughput... |
| compress-BindScore | Compress BindScore Objects |
| compress-methods | Methods for Function compress in Package 'ChIPseqR' |
| compress-ReadCounts | Compress ReadCount Objects |
| decompress | 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 |
| internal | Internal and undocumented functions |
| pickPeak | Identify peaks above a given threshold |
| plot-BindScore | Diagnostic Plots for Binding Site Scores |
| plot-ReadCounts | Diagnostic Plots for Read Counts |
| plotReads | Plot compact representation of read counts on a chromosome |
| plotWindow | Plot read counts within a genomic region |
| pos2gff | Convert genome coordinates into GFF format |
| ReadCounts | Class "ReadCounts" |
| RLEBindScore-class | Run-length Encoded Binding Site Scores |
| RLEReadCounts-class | Run-length Encoded Read Counts |
| simpleNucCall | Predict nucleosome positions from high-throughput sequencing... |
| startScore | Score potential protein binding sites |
| strandPileup | Strand specific read counts |
| windowCounts | Summarize read counts in a sliding window |
