Package: rhierbaps 1.1.3
rhierbaps: Clustering Genetic Sequence Data Using the HierBAPS Algorithm
Implements the hierarchical Bayesian analysis of populations structure (hierBAPS) algorithm of Cheng et al. (2013) <doi:10.1093/molbev/mst028> for clustering DNA sequences from multiple sequence alignments in FASTA format. The implementation includes improved defaults and plotting capabilities and unlike the original 'MATLAB' version removes singleton SNPs by default.
Authors:
rhierbaps_1.1.3.tar.gz
rhierbaps_1.1.3.zip(r-4.5)rhierbaps_1.1.3.zip(r-4.4)rhierbaps_1.1.3.zip(r-4.3)
rhierbaps_1.1.3.tgz(r-4.4-any)rhierbaps_1.1.3.tgz(r-4.3-any)
rhierbaps_1.1.3.tar.gz(r-4.5-noble)rhierbaps_1.1.3.tar.gz(r-4.4-noble)
rhierbaps_1.1.3.tgz(r-4.4-emscripten)rhierbaps_1.1.3.tgz(r-4.3-emscripten)
rhierbaps.pdf |rhierbaps.html✨
rhierbaps/json (API)
NEWS
| # Install 'rhierbaps' in R: |
| install.packages('rhierbaps', repos = c('https://gtonkinhill.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gtonkinhill/rhierbaps/issues
population-geneticspopulation-genomicspopulation-structure
Last updated 4 years agofrom:8480ef5d27. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 02 2024 |
| R-4.5-win | OK | Nov 02 2024 |
| R-4.5-linux | OK | Nov 02 2024 |
| R-4.4-win | OK | Nov 02 2024 |
| R-4.4-mac | OK | Nov 02 2024 |
| R-4.3-win | OK | Nov 02 2024 |
| R-4.3-mac | OK | Nov 02 2024 |
Exports:hierBAPSload_fastaplot_sub_clustersave_lml_logs
Dependencies:apeclicolorspacedigestfansifarverggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmatrixStatsmgcvmunsellnlmepatchworkpillarpkgconfigpurrrR6RColorBrewerRcpprlangscalestibbleutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| calc_change_in_ml | calc_change_in_ml |
| calc_log_ml | calc_log_ml |
| hierBAPS | hierBAPS |
| join_units_2 | join_units_2 |
| load_fasta | load_fasta |
| model_search_parallel | model_search_parallel |
| move_units_1 | move_units_1 |
| plot_sub_cluster | plot_sub_cluster |
| preproc_alignment | preproc_alignment |
| reallocate_units_4 | reallocate_units_4 |
| save_lml_logs | save_lml_logs |
| split_clusters_3 | split_clusters_3 |
