TFHAZ

DOI: 10.18129/B9.bioc.TFHAZ  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see TFHAZ.

Transcription Factor High Accumulation Zones

Bioconductor version: 3.16

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>

Installation

To install this package, start R (version "4.2") and enter:

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

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")

 

HTML	R Script	TFHAZ
PDF		Reference Manual

Details

biocViews	BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription
Version	1.20.0
In Bioconductor since	BioC 3.6 (R-3.4) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods, ORFik
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	TFHAZ_1.20.0.tar.gz
Windows Binary	TFHAZ_1.20.0.zip
macOS Binary (x86_64)	TFHAZ_1.20.0.tgz
macOS Binary (arm64)	TFHAZ_1.20.0.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