TFHAZ

DOI: 10.18129/B9.bioc.TFHAZ    

Transcription Factor High Accumulation Zones

Bioconductor version: Release (3.6)

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. Then, high accumulation DNA zones are defined as regions of the genome formed by contiguous bases with accumulation equal or higher than a given threshold. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

Author: Alberto Marchesi, Marco Masseroli

Maintainer: Alberto Marchesi <alberto.march91 at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("TFHAZ")

Documentation

HTML	R Script	TFHAZ
PDF		Reference Manual

Details

biocViews	BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription
Version	1.0.0
License	Artistic-2.0
Depends	R (>= 3.4)
Imports	GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Source Package	TFHAZ_1.0.0.tar.gz
Windows Binary	TFHAZ_1.0.0.zip
Mac OS X 10.11 (El Capitan)	TFHAZ_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/TFHAZ
Package Short Url	http://bioconductor.org/packages/TFHAZ/
Package Downloads Report	Download Stats