BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis.
|Author||Ahrim Youn [aut, cre], Eladio Marquez [aut], Nathan Lawlor [aut], Michael Stitzel [aut], Duygu Ucar [aut]|
|Bioconductor views||ATACSeq DNaseSeq Epigenetics GeneRegulation Genetics RIPSeq Software Transcription|
|Date of publication||2018-07-15|
|Maintainer||Ahrim Youn <[email protected]>|
|Package repository||View on Bioconductor|
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