TFHAZ
Transcription Factor High Accumulation Zones
Bioconductor version: 3.24 · Package version: 1.35.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("TFHAZ")Details
| Maintainer | Gaia Ceddia <gaia.ceddia@polimi.it> |
| Author | Alberto Marchesi, Silvia Cascianelli, Marco Masseroli |
| License | Artistic-2.0 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | BiologicalQuestion, ChIPSeq, Coverage, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/TFHAZ/ |
Citation
From within R, enter citation("TFHAZ"):
Alberto Marchesi, Silvia Cascianelli, Marco Masseroli. TFHAZ: Transcription Factor High Accumulation Zones. doi:10.18129/B9.bioc.TFHAZ, R package version 1.35.0, https://bioconductor.org/packages/TFHAZ.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | TFHAZ_1.35.0.tar.gz |
| Windows binary (x86_64) | TFHAZ_1.35.0.zip |
| macOS binary (arm64) | TFHAZ_1.35.0.tgz |
| macOS binary (x86_64) | TFHAZ_1.35.0.tgz |