BiFET: Bias-free Footprint Enrichment Test
Version 1.0.1

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.

Package details

AuthorAhrim Youn [aut, cre], Eladio Marquez [aut], Nathan Lawlor [aut], Michael Stitzel [aut], Duygu Ucar [aut]
Bioconductor views ATACSeq DNaseSeq Epigenetics GeneRegulation Genetics RIPSeq Software Transcription
Date of publication2018-07-15
MaintainerAhrim Youn <[email protected]>
LicenseGPL-3
Version1.0.1
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BiFET")

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BiFET documentation built on July 17, 2018, 6 p.m.