scoup
This is the development version of scoup; for the stable release version, see scoup.
Simulate Codons with Darwinian Selection Modelled as an OU Process
Bioconductor version: Development (3.21)
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.
Author: Hassan Sadiq [aut, cre, cph] (ORCID:
Maintainer: Hassan Sadiq <hassan.t.sadiq at gmail.com>
citation("scoup")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("scoup")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("scoup")| scoup Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Classification, ComparativeGenomics, DataImport, Genetics, MathematicalBiology, ResearchField, SequenceMatching, Sequencing, Software, StatisticalMethod, WorkflowStep |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| License | GPL (>= 2) |
| Depends | R (>= 4.4), Matrix |
| Imports | Biostrings, methods |
| System Requirements | |
| URL | https://github.com/thsadiq/scoup |
| Bug Reports | https://github.com/thsadiq/scoup/issues |
See More
| Suggests | BiocManager, BiocStyle, bookdown, htmltools, knitr, testthat (>= 3.0.0), yaml |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scoup_1.1.0.tar.gz |
| Windows Binary (x86_64) | scoup_1.1.0.zip |
| macOS Binary (x86_64) | scoup_1.1.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/scoup |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scoup |
| Bioc Package Browser | https://code.bioconductor.org/browse/scoup/ |
| Package Short Url | https://bioconductor.org/packages/scoup/ |
| Package Downloads Report | Download Stats |