Package: protHMM
Type: Package
Title: Protein Feature Extraction from Profile Hidden Markov Models
Version: 0.1.1
Authors@R: person("Shayaan", "Emran", email = "shayaan.emran@gmail.com", role = c("aut", "cre", "cph"))
Maintainer: Shayaan Emran <shayaan.emran@gmail.com>
Description: Calculates a comprehensive list of features from profile
        hidden Markov models (HMMs) of proteins. Adapts and ports
        features for use with HMMs instead of Position Specific Scoring
        Matrices, in order to take advantage of more accurate multiple
        sequence alignment by programs such as 'HHBlits'
        <DOI:10.1038/nmeth.1818> and 'HMMer' <http://hmmer.org>.
        Features calculated by this package can be used for protein
        fold classification, protein structural class prediction,
        sub-cellular localization and protein-protein interaction,
        among other tasks. Some examples of features extracted are
        found in Song et al. (2018) <DOI:10.3390/app8010089>, Jin & Zhu
        (2021) <DOI:10.1155/2021/8629776>, Lyons et al. (2015)
        <DOI:10.1109/tnb.2015.2457906> and Saini et al. (2015)
        <DOI:10.1016/j.jtbi.2015.05.030>.
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 7.2.3
Imports: gtools, utils, stats, phonTools
Suggests: covr, knitr, rmarkdown, testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
URL: https://github.com/semran9/protHMM/,
        https://semran9.github.io/protHMM/
BugReports: https://github.com/semran9/protHMM/issues
Repository: https://semran9.r-universe.dev
Date/Publication: 2023-09-11 00:26:19 UTC
RemoteUrl: https://github.com/semran9/prothmm
RemoteRef: HEAD
RemoteSha: c87243606574287e068b584d4eca5ec86f6df25c
NeedsCompilation: no
Packaged: 2026-10-10 07:42:05 UTC; root
Author: Shayaan Emran [aut, cre, cph]