TFHAZ

DOI: 10.18129/B9.bioc.TFHAZ    

Transcription Factor High Accumulation Zones

Bioconductor version: Release (3.8)

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, Marco Masseroli

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

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("TFHAZ", version = "3.8")

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 1.4.0
License Artistic-2.0
Depends R (>= 3.4)
Imports GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges, methods
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_1.4.0.tar.gz
Windows Binary TFHAZ_1.4.0.zip
Mac OS X 10.11 (El Capitan) TFHAZ_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/TFHAZ
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/TFHAZ
Package Short Url http://bioconductor.org/packages/TFHAZ/
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