queeems
Quantify the Extent of Evolutionary Evidence in Molecular Sequences
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("queeems")Details
| Maintainer | Hassan Sadiq <hassan.t.sadiq@gmail.com> |
| Author | Hassan Sadiq [aut, cre, cph, fnd] (ORCID: <https://orcid.org/0000-0003-0192-7134>) |
| License | GPL-3 + file LICENSE |
| URL | https://github.com/thsadiq/queeems |
| Bug Reports | https://github.com/thsadiq/queeems/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Bayesian, Classification, DataImport, Genetics, MathematicalBiology, ResearchField, SequenceMatching, Sequencing, Software, StatisticalMethod, WorkflowStep |
| Package Short Url | https://bioconductor.org/packages/queeems/ |
Citation
From within R, enter 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.
Documentation
Download
Follow the 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 (arm64) | queeems_1.0.0.tgz |
| macOS binary (x86_64) | queeems_1.0.0.tgz |
Dependencies
Depends: R (>= 4.5.0), Biostrings
Imports: gtools, Matrix, methods, stats
Suggests: BiocStyle, knitr, testthat (>= 3.0.0)