bPeaks: bPeaks: an intuitive peak-calling strategy to detect transcription factor binding sites from ChIP-seq data in small eukaryotic genomes
bPeaks is a simple approach to identify transcription factor binding sites from ChIP-seq data. Our general philosophy is to provide an easy-to-use tool, well-adapted for small eukaryotic genomes (< 20 Mb). bPeaks uses a combination of 4 cutoffs (T1, T2, T3 and T4) to mimic "good peak" properties as described by biologists who visually inspect the ChIP-seq data on a genome browser. For yeast genomes, bPeaks calculates the proportion of peaks that fall in promoter sequences. These peaks are good candidates as transcription factor binding sites.
- Jawad MERHEJ and Gaelle LELANDAIS
- Date of publication
- 2014-02-28 17:55:13
- Gaelle LELANDAIS <firstname.lastname@example.org>
- Function to calculate the average number of reads mapped on...
- Function to run the entire bPeaks procedure
- bPeaks: an intuitive peak-calling strategy to detect...
- ChIP-seq results (IP and control samples) obtained with the...
- Function to import sequencing results in R
- Function to smooth sequencing coverage along a chromosome
- Peak calling method, i. e. identification of genomic regions...
- Function to draw graphical representations of genomic regions...
- Function to locate detected basic peaks (bPeaks) according to...
- Annotations of CDS for different yeast species
Files in this package