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 Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=shazam to link to this page.
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