queeems
This is the released version of queeems; for the devel version, see queeems.
Quantify the Extent of Evolutionary Evidence in Molecular Sequences
Bioconductor version: Release (3.23)
Biological inferences obtained from molecular data are only as good as the extent of evolutionary signatures retained in the genetic data. Techniques available to quantify these signatures are largely targeted towards phylogeny reconstruction and they often rely on adhoc hypothesis tests of significance. I present a Bayesian function that assesses whether a set of genetic sequences are saturated. That is, it is useful for determining whether the evolutionary information in the sequences has eroded with time. Site specific Bayes factors are generated with respect to codon bases to allow for straightforward applications in extensive computational biology inquiries, including natural selection analyses.
Author: Hassan Sadiq [aut, cre, cph, fnd] 
Maintainer: Hassan Sadiq <hassan.t.sadiq at gmail.com>
citation("queeems")):Hassan Sadiq. queeems: Quantify the Extent of Evolutionary Evidence in Molecular Sequences. doi:10.18129/B9.bioc.queeems, R package version 1.0.0, https://bioconductor.org/packages/queeems.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("queeems")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("queeems")| queeems Tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Alignment, Bayesian, Classification, DataImport, Genetics, MathematicalBiology, ResearchField, SequenceMatching, Sequencing, Software, StatisticalMethod, WorkflowStep |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.5.0), Biostrings |
| Imports | gtools, Matrix, methods, stats |
| System Requirements | |
| URL | https://github.com/thsadiq/queeems |
| Bug Reports | https://github.com/thsadiq/queeems/issues |
See More
| Suggests | BiocStyle, knitr, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | queeems_1.0.0.tar.gz |
| Windows Binary (x86_64) | queeems_1.0.0.zip |
| macOS Binary (big-sur-x86_64) | queeems_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | queeems_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/queeems |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/queeems |
| Package Short Url | https://bioconductor.org/packages/queeems/ |
| Package Downloads Report | Download Stats |