Man pages for ChIPseqR
Identifying Protein Binding Sites in High-Throughput Sequencing Data

accessorsAccess slots of S4 classes
alignFeatureRead counts relative to annotated features
BindScoreClass "BindScore"
callBindingSitesPredict protein binding sites from high-throughput sequencing...
ChIPseqR-packageIdentifying Protein Binding Sites in High-Throughput...
compress-BindScoreCompress BindScore Objects
compress-methodsMethods for Function compress in Package 'ChIPseqR'
compress-ReadCountsCompress ReadCount Objects
decompressExtract Read Count and Binding Site Score Representations
decompress-methodsMethods for Function decompress in Package 'ChIPseqR'
exportBindSequenceExport sequence of predicted binding sites
getBindCorCalculate cross-correlation between read counts
getBindLenEstimate length of binding and support region
getCutoffDetermine significance threshold for binding site scores
internalInternal and undocumented functions
pickPeakIdentify peaks above a given threshold
plot-BindScoreDiagnostic Plots for Binding Site Scores
plot-ReadCountsDiagnostic Plots for Read Counts
plotReadsPlot compact representation of read counts on a chromosome
plotWindowPlot read counts within a genomic region
pos2gffConvert genome coordinates into GFF format
ReadCountsClass "ReadCounts"
RLEBindScore-classRun-length Encoded Binding Site Scores
RLEReadCounts-classRun-length Encoded Read Counts
simpleNucCallPredict nucleosome positions from high-throughput sequencing...
startScoreScore potential protein binding sites
strandPileupStrand specific read counts
windowCountsSummarize read counts in a sliding window
ChIPseqR documentation built on Nov. 8, 2020, 6:49 p.m.