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: | 1.2.0 |
| Depends: | R (≥ 4.0), ggplot2 (≥ 3.4.0) |
| Imports: | alakazam (≥ 1.3.0), 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 |
| Published: | 2023-10-02 |
| 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://bitbucket.org/kleinstein/shazam/issues |
| License: | AGPL-3 |
| URL: | http://shazam.readthedocs.io |
| NeedsCompilation: | no |
| Citation: | shazam citation info |
| Materials: | README NEWS |
| CRAN checks: | shazam results |
| Reference manual: | shazam.pdf |
| Vignettes: |
Selection quantification Distance to nearest neighbor Mutation analysis Simulating sequence mutations SHM targeting models |
| Package source: | shazam_1.2.0.tar.gz |
| Windows binaries: | r-devel: shazam_1.2.0.zip, r-release: shazam_1.2.0.zip, r-oldrel: shazam_1.2.0.zip |
| macOS binaries: | r-release (arm64): shazam_1.2.0.tgz, r-oldrel (arm64): shazam_1.2.0.tgz, r-release (x86_64): shazam_1.2.0.tgz, r-oldrel (x86_64): shazam_1.2.0.tgz |
| Old sources: | shazam archive |
| Reverse imports: | dowser, scoper |
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