Package: BiFET
Type: Package
Title: Bias-free Footprint Enrichment Test
Version: 1.33.0
Date: 2025-06-27
Authors@R: c(person("Ahrim", "Youn", email = "Ahrim.Youn@jax.org",
    role = c("aut", "cre")), person("Eladio", "Marquez",
    email = "Eladio.Marquez@jax.org", role = c("aut")), 
    person("Nathan",  "Lawlor", email = "nathan.lawlor03@gmail.com", 
    role = c("aut")), person("Michael", "Stitzel",
    email = "Michael.Stitzel@jax.org", role = c("aut")),person("Duygu",
    "Ucar", email = "Duygu.Ucar@jax.org", role = c("aut")))
Maintainer: Ahrim Youn <Ahrim.Youn@jax.org>
Description: 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.
License: GPL-3
biocViews: ImmunoOncology, Genetics, Epigenetics, Transcription,
        GeneRegulation, ATACSeq, DNaseSeq, RIPSeq, Software
Encoding: UTF-8
RoxygenNote: 6.0.1
Imports: stats, poibin, GenomicRanges
Suggests: rmarkdown, testthat, knitr
VignetteBuilder: knitr
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:47:07 UTC
RemoteUrl: https://github.com/bioc/BiFET
RemoteRef: HEAD
RemoteSha: e6d1543055fc5419354db78e4e38049463b9c6ad
NeedsCompilation: no
Packaged: 2026-07-07 06:04:21 UTC; root
Author: Ahrim Youn [aut, cre],
  Eladio Marquez [aut],
  Nathan Lawlor [aut],
  Michael Stitzel [aut],
  Duygu Ucar [aut]
Depends: R (>= 3.5.0)