TFHAZ
This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see TFHAZ.
Transcription Factor High Accumulation Zones
Bioconductor version: 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>
citation("TFHAZ")):
Installation
To install this package, start R (version "3.4") 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
| Reference Manual |
Details
| biocViews | BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (6.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.4) |
| Imports | GenomicRanges, S4Vectors, grDevices, graphics, stats, utils, IRanges |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown |
| 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 | 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 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/TFHAZ |
| Package Short Url | https://bioconductor.org/packages/TFHAZ/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.6 | Source Archive |