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BiFET

Bias-free Footprint Enrichment Test


Bioconductor version: Release (3.18)

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 jax.org>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiFET")

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

Documentation

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

browseVignettes("BiFET")
A Guide to using BiFET HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews ATACSeq, DNaseSeq, Epigenetics, GeneRegulation, Genetics, ImmunoOncology, RIPSeq, Software, Transcription
Version 1.22.0
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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Suggests rmarkdown, testthat, knitr
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package BiFET_1.22.0.tar.gz
Windows Binary BiFET_1.22.0.zip (64-bit only)
macOS Binary (x86_64) BiFET_1.22.0.tgz
macOS Binary (arm64) BiFET_1.22.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiFET
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiFET
Bioc Package Browser https://code.bioconductor.org/browse/BiFET/
Package Short Url https://bioconductor.org/packages/BiFET/
Package Downloads Report Download Stats