BiFET
This is the development version of BiFET; for the stable release version, see BiFET.
Bias-free Footprint Enrichment Test
Bioconductor version: Development (3.24)
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("BiFET")):Ahrim Youn, Eladio Marquez, Nathan Lawlor, Michael Stitzel, Duygu Ucar. BiFET: Bias-free Footprint Enrichment Test. doi:10.18129/B9.bioc.BiFET, R package version 1.33.0, https://bioconductor.org/packages/BiFET.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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")| A Guide to using BiFET | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, DNaseSeq, Epigenetics, GeneRegulation, Genetics, ImmunoOncology, RIPSeq, Software, Transcription |
| Version | 1.33.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | stats, poibin, GenomicRanges |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, testthat, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiFET_1.33.0.tar.gz |
| Windows Binary (x86_64) | BiFET_1.33.0.zip |
| macOS Binary (big-sur-x86_64) | BiFET_1.33.0.tgz |
| macOS Binary (sonoma-arm64) | BiFET_1.33.0.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 |