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BiFET

Bias-free Footprint Enrichment Test (BiFET) is a statistical method to identify transcription factors (TFs) whose footprints are over-represented in target regions compared to background regions after correcting for differences in read counts and GC contents between target and background regions, where regions represent ATAC-seq or DNAse-seq peaks.

Author

Ahrim Youn

Installation:

To install this package, start R and enter:

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

BiocManager::install("BiFET")

Alternatively, the most updated version of this package may be installed via the commands in R:

library(devtools)

install_github('UcarLab/BiFET')

Publication:

For more details about BiFET, please read our publication in Nucleic Acids Research: https://www.ncbi.nlm.nih.gov/pubmed/30428075

Tutorial:

For instructions on how to use BiFET, please see the package vignette: https://bioconductor.org/packages/release/bioc/vignettes/BiFET/inst/doc/BiFET.html

Disclaimer of Warranties and Liabilities

The Jackson Laboratory provides the software “as is” without warranty of any kind, implied or expressed. You assume full responsibility and risk of loss resulting from your downloading and use of the content of the software. We expressly disclaim any warranty of merchantability, title, security, accuracy and non-infringement. In no event shall The Jackson Laboratory be liable for any claim, damages or other liability arising from the software or the use of the software. You may only use our content in academic research but not for commercial purposes. The software is provided as an information resource only, and should not be used or relied on for any diagnostic or treatment purposes.

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