BiFET

DOI: 10.18129/B9.bioc.BiFET    

This is the development version of BiFET; for the stable release version, see BiFET.

Bias-free Footprint Enrichment Test

Bioconductor version: Development (3.8)

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 and enter:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("BiFET", version = "devel")

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, RIPSeq, Software, Transcription
Version 1.1.6
License GPL-3
Depends
Imports stats, poibin, GenomicRanges
LinkingTo
Suggests testthat, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package BiFET_1.1.6.tar.gz
Windows Binary BiFET_1.1.6.zip
Mac OS X 10.11 (El Capitan) BiFET_1.1.6.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 http://bioconductor.org/packages/BiFET/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: