Package: scoup
Version: 1.0.0
Date: 2024-10-23
License: GPL (>= 2)
Authors@R: c(person("Hassan", "Sadiq", role=c("aut","cre","cph"),
                    email="hassan.t.sadiq@gmail.com",
                    comment=c(ORCID="0000-0003-0192-7134")))
Title: Simulate Codons with Darwinian Selection Modelled as an OU
        Process
Description: An elaborate molecular evolutionary framework that facilitates
             straightforward simulation of codon genetic sequences
             subjected to different degrees and/or patterns of Darwinian
             selection. The model was built upon the fitness landscape
             paradigm of Sewall Wright, as popularised by the
             mutation-selection model of Halpern and Bruno. This
             enabled realistic evolutionary process of living organisms
             to be reproduced seamlessly. For example, an
             Ornstein-Uhlenbeck fitness update algorithm is incorporated
             herein. Consequently, otherwise complex biological processes,
             such as the effect of the interplay between genetic drift
             and mutation on the inference of diversifying selection, may
             now be investigated with minimal effort. Frequency-dependent
             and deterministic fitness landscape update techniques are
             also available.
Depends: R (>= 4.4), Matrix
Imports: Biostrings, methods
Suggests: BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat
        (>= 3.0.0), yaml
VignetteBuilder: knitr
Config/testthat/edition: 3
biocViews: Alignment, Classification, ComparativeGenomics, DataImport,
        Genetics, MathematicalBiology, ResearchField, Sequencing,
        SequenceMatching, Software, StatisticalMethod, WorkflowStep
Contact: <hassan.t.sadiq@gmail.com>
URL: https://github.com/thsadiq/scoup
BugReports: https://github.com/thsadiq/scoup/issues
Packaged: 2024-10-30 02:43:24 UTC; biocbuild
git_url: https://git.bioconductor.org/packages/scoup
git_branch: RELEASE_3_20
git_last_commit: 0bd7126
git_last_commit_date: 2024-10-29
Repository: Bioconductor 3.20
Date/Publication: 2024-10-29
NeedsCompilation: no
Author: Hassan Sadiq [aut, cre, cph] (<https://orcid.org/0000-0003-0192-7134>)
Maintainer: Hassan Sadiq <hassan.t.sadiq@gmail.com>
