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Bias-free Footprint Enrichment Test

Bioconductor version: Release (3.19)

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>

Citation (from within R, enter citation("BiFET")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

A Guide to using BiFET HTML R Script
Reference Manual PDF


biocViews ATACSeq, DNaseSeq, Epigenetics, GeneRegulation, Genetics, ImmunoOncology, RIPSeq, Software, Transcription
Version 1.24.0
In Bioconductor since BioC 3.7 (R-3.5) (6 years)
License GPL-3
Depends R (>= 3.5.0)
Imports stats, poibin, GenomicRanges
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Source Package BiFET_1.24.0.tar.gz
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macOS Binary (x86_64) BiFET_1.24.0.tgz
macOS Binary (arm64) BiFET_1.24.0.tgz
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