bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes


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Documentation for package ‘bPeaks’ version 1.2

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bPeaks-package bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes
baseLineCalc Function to calculate the average number of reads mapped on each nucleotide in a genome
bPeaks bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes
bPeaksAnalysis Function to run the entire bPeaks procedure
dataPDR1 ChIP-seq results (IP and control samples) obtained with the transcription factor Pdr1 in yeast Saccharomyces cerevisiae
dataReading Function to import sequencing results in R
dataSmoothing Function to smooth sequencing coverage along a chromosome
peakDetection Peak calling method, i. e. identification of genomic regions with a high density of sequences (reads)
peakDrawing Function to draw graphical representations of genomic regions detected using bPeaks methodology
peakLocation Function to locate detected basic peaks (bPeaks) according to predifined chromosomal features
yeastCDS Annotations of CDS for different yeast species