Package: NuPoP
Type: Package
Title: An R package for nucleosome positioning prediction
Version: 2.17.0
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
git_url: https://git.bioconductor.org/packages/NuPoP
git_branch: devel
git_last_commit: b350a81
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-10-07
Packaged: 2025-10-07 23:07:46 UTC; biocbuild
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-29 16:38:20 UTC; windows
Archs: x64
