DOI: 10.18129/B9.bioc.BiFET    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see BiFET.

Bias-free Footprint Enrichment Test

Bioconductor version: 3.8

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]

Maintainer: Ahrim Youn <Ahrim.Youn at>

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biocViews ATACSeq, DNaseSeq, Epigenetics, GeneRegulation, Genetics, ImmunoOncology, RIPSeq, Software, Transcription
Version 1.2.1
In Bioconductor since BioC 3.7 (R-3.5) (1 year)
License GPL-3
Imports stats, poibin, GenomicRanges
Suggests testthat, knitr
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