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>
citation("TFHAZ")):
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")| TFHAZ | HTML | R Script |
| Reference Manual |
Details
| biocViews | BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription |
| Version | 1.20.0 |
| 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 |
| 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_1.20.0.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 |
| Old Source Packages for BioC 3.16 | Source Archive |