Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.
| Version: | 1.3.0 |
| Depends: | R (≥ 4.0),ggplot2 (≥ 3.4.0) |
| Imports: | alakazam (≥ 1.4.1),ape,diptest,doParallel,dplyr (≥ 1.0),foreach, graphics, grid,igraph (≥ 1.5.0),iterators,KernSmooth,lazyeval,MASS, methods, parallel,progress,rlang,scales,seqinr, stats,stringi (≥ 1.1.3),tidyr,tidyselect, utils |
| Suggests: | knitr,rmarkdown,testthat,tibble |
| Published: | 2025-10-20 |
| DOI: | 10.32614/CRAN.package.shazam |
| Author: | Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut, cre], Julian Zhou [aut], Nima Nouri [aut], Noah Yann Lee [aut], Ang Cui [ctb], Jason Vander Heiden [aut], Gur Yaari [aut], Steven Kleinstein [aut, cph] |
| Maintainer: | Susanna Marquez <susanna.marquez at yale.edu> |
| BugReports: | https://github.com/immcantation/shazam/issues |
| License: | AGPL-3 |
| URL: | http://shazam.readthedocs.io |
| NeedsCompilation: | no |
| Citation: | shazam citation info |
| Materials: | README,NEWS |
| CRAN checks: | shazam results[issues need fixing before 2026-01-15] |