Provides functions to quantify dominant clonal lineages from DNA barcoding time-series data. The package implements clustering of barcode lineage trajectories, based on the assumption that similar temporal dynamics indicate comparable relative fitness. It also identifies persistent clonal lineages across time points. Input data can include lineage frequency tables derived from chromosomal barcoding, mutational libraries, or CRISPR/Cas screens. For more details, see Gagné-Leroux et al. (2024) <doi:10.1101/2024.09.08.611892>.
| Version: |
0.1.1 |
| Imports: |
entropy, gplots, lazyeval, proxy, grid, ggthemes, ggplot2, magrittr, dplyr, ggnewscale, readr, data.table, reshape2, grDevices, stats, imputeTS, dtwclust, purrr, tidyr, TSdist, graphics |
| Suggests: |
knitr, rmarkdown, testthat (≥ 3.0.0), devtools, ggpubr, optparse, pryr |
| Published: |
2025-05-21 |
| Author: |
Adrian Serohijos [aut, cre],
David Gagné-Leroux [ctb],
Melis Gencel [ctb],
Louis Gauthier [ctb] |
| Maintainer: |
Adrian Serohijos <adrian.serohijos at umontreal.ca> |
| License: |
GPL-3 |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
doblin results |