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TFHAZ

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

Transcription Factor High Accumulation Zones


Bioconductor version: Development (3.20)

It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

Author: Alberto Marchesi, Silvia Cascianelli, Marco Masseroli

Maintainer: Gaia Ceddia <gaia.ceddia at polimi.it>

Citation (from within R, enter citation("TFHAZ")):

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("TFHAZ")

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("TFHAZ")
TFHAZ HTML R Script
Reference Manual PDF

Details

biocViews BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription
Version 1.27.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik
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Package Archives

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

Source Package TFHAZ_1.27.0.tar.gz
Windows Binary TFHAZ_1.27.0.zip (64-bit only)
macOS Binary (x86_64) TFHAZ_1.27.0.tgz
macOS Binary (arm64) TFHAZ_1.27.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TFHAZ
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TFHAZ
Bioc Package Browser https://code.bioconductor.org/browse/TFHAZ/
Package Short Url https://bioconductor.org/packages/TFHAZ/
Package Downloads Report Download Stats