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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 |
Please use the canonical form https://CRAN.R-project.org/package=shazam to link to this page.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.