Package: NuPoP
Type: Package
Title: An R package for nucleosome positioning prediction
Version: 2.19.0
Date: 2020-11-21
Author: Ji-Ping Wang <jzwang@northwestern.edu>; Liqun Xi
        <liqunxi02@gmail.com>; Oscar Zarate <zarate@u.northwestern.edu>
Maintainer: Ji-Ping Wang<jzwang@northwestern.edu>
Description: NuPoP is an R package for Nucleosome Positioning
        Prediction.This package is built upon a duration hidden Markov
        model proposed in Xi et al, 2010; Wang et al, 2008. The core of
        the package was written in Fotran. In addition to the R
        package, a stand-alone Fortran software tool is also available
        at https://github.com/jipingw. The Fortran codes have complete
        functonality as the R package.  Note: NuPoP has two separate
        functions for prediction of nucleosome positioning, one for
        MNase-map trained models and the other for chemical map-trained
        models. The latter was implemented for four species including
        yeast, S.pombe, mouse and human, trained based on our recent
        publications. We noticed there is another package nuCpos by
        another group for prediction of nucleosome positioning trained
        with chemicals. A report to compare recent versions of NuPoP
        with nuCpos can be found at
        https://github.com/jiping/NuPoP_doc. Some more information can
        be found and will be posted at
        https://github.com/jipingw/NuPoP.
License: GPL-2
Imports: graphics, utils
biocViews: Genetics,Visualization,Classification,NucleosomePositioning,
        HiddenMarkovModel
Depends: R (>= 4.0)
NeedsCompilation: yes
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 14:05:35 UTC
RemoteUrl: https://github.com/bioc/NuPoP
RemoteRef: HEAD
RemoteSha: 095144bf4b768e9a2c513baa3d799426bab5b3c2
Packaged: 2026-01-22 19:40:44 UTC; root
Built: R 4.6.0; aarch64-apple-darwin23; 2026-01-22 20:03:20 UTC; unix
