BiFET
This is the development version of BiFET; for the stable release version, see BiFET.
Bias-free Footprint Enrichment Test
Bioconductor version: Development (3.20)
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")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.25.0 |
In Bioconductor since | BioC 3.7 (R-3.5) (6.5 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | BiFET_1.25.0.tar.gz |
Windows Binary | BiFET_1.25.0.zip |
macOS Binary (x86_64) | BiFET_1.25.0.tgz |
macOS Binary (arm64) | BiFET_1.25.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/BiFET |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiFET |
Bioc Package Browser | https://code.bioconductor.org/browse/BiFET/ |
Package Short Url | https://bioconductor.org/packages/BiFET/ |
Package Downloads Report | Download Stats |