BiFET

DOI: 10.18129/B9.bioc.BiFET    

Bias-free Footprint Enrichment Test

Bioconductor version: Release (3.13)

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 "4.1") and enter:

if (!requireNamespace("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	1.12.0
In Bioconductor since	BioC 3.7 (R-3.5) (3.5 years)
License	GPL-3
Depends
Imports	stats, poibin, GenomicRanges
LinkingTo
Suggests	testthat, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BiFET_1.12.0.tar.gz
Windows Binary	BiFET_1.12.0.zip
macOS 10.13 (High Sierra)	BiFET_1.12.0.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