Package: TFHAZ
Type: Package
Title: Transcription Factor High Accumulation Zones
Version: 1.32.0
Author: Alberto Marchesi, Silvia Cascianelli, Marco Masseroli
Maintainer: Gaia Ceddia <gaia.ceddia@polimi.it>
Description: 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.
License: Artistic-2.0
Encoding: UTF-8
Imports: GenomicRanges, S4Vectors, grDevices, graphics, stats, utils,
        IRanges, methods, ORFik
biocViews: Software, BiologicalQuestion, Transcription, ChIPSeq,
        Coverage
LazyData: true
Depends: R (>= 3.5.0)
Suggests: BiocStyle, knitr, rmarkdown
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev libx11-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:40:39 UTC
RemoteUrl: https://github.com/bioc/TFHAZ
RemoteRef: RELEASE_3_22
RemoteSha: c615f9e59122de487d24e97a8f88e5c06c20bbb7
NeedsCompilation: no
Packaged: 2025-11-11 18:06:31 UTC; root
Built: R 4.5.2; ; 2025-11-11 18:13:38 UTC; windows
