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ChIPComp is an R library performing the differential binding analysis for ChIP-seq count data. Compared with other similar packages (DBChIP, DIME), ChIPComp considers the control samples in the process of detecting the differential binding sites. Extensive simulation results showed that ChIPComp performs favorably compared to DBChIP and DIME when the control samples are ignored. ChIPComp only works for two group comparison at this time, that is, to detect the differential binding sites for one transcription factor(histone) between two conditions (cell lines). We plan to extend the functionalities and make it work for more general experimental designs in the near future.
● Data Source:
BioConductor
● Keywords: package
● Alias: ChIPComp-package
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Perform hypothesis testing to detect differential binding sites
● Data Source:
BioConductor
● Keywords:
● Alias: ChIPComp
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makeConf
(Package: ChIPComp) :
make configurations for experimental design written in csv sheet
Make a list with two elements. The first element is a data frame containing two group comparison study information. The second element is the design matrix.
● Data Source:
BioConductor
● Keywords:
● Alias: makeConf
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makeCountSet
(Package: ChIPComp) :
make differential binding sites data frame
This is an utility function to create a data frame. The data frame contains binding sites merged by peaks from two conditions, count ChIP read counts, smoothing control counts for each candidate region, and indicate the common peaks from two conditions.
● Data Source:
BioConductor
● Keywords:
● Alias: makeCountSet
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plot.ChIPComp
(Package: ChIPComp) :
plot correlation between log ChIP read counts and smoothing control counts in common binding sites.
plot correlation between log ChIP counts and smoothing control counts in common binding sites.
● Data Source:
BioConductor
● Keywords:
● Alias: plot.ChIPComp
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Print top differential binding sites ranked by posterior probability in a decreasing order.
● Data Source:
BioConductor
● Keywords:
● Alias: print.ChIPComp
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providing 
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