BiFET

DOI: 10.18129/B9.bioc.BiFET    

Bias-free Footprint Enrichment Test

Bioconductor version: Release (3.15)

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	A Guide to using BiFET
PDF		Reference Manual
Text		NEWS

Details

biocViews	ATACSeq, DNaseSeq, Epigenetics, GeneRegulation, Genetics, ImmunoOncology, RIPSeq, Software, Transcription
Version	1.16.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	GPL-3
Depends	R (>= 3.5.0)
Imports	stats, poibin, GenomicRanges
LinkingTo
Suggests	rmarkdown, testthat, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report

Package Archives

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

Source Package	BiFET_1.16.0.tar.gz
Windows Binary	BiFET_1.16.0.zip
macOS Binary (x86_64)	BiFET_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiFET
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiFET
Package Short Url	https://bioconductor.org/packages/BiFET/
Package Downloads Report	Download Stats