Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires.
| Version: | 0.1.8 |
| Depends: | R (≥ 3.1.2), ggplot2 (≥ 2.0.0) |
| Imports: | alakazam (≥ 0.2.6), ape, diptest, doParallel, dplyr (≥ 0.5.0), foreach, graphics, grid, igraph, iterators, kedd, KernSmooth, lazyeval, MASS, methods, parallel, progress, SDMTools, scales, seqinr, stats, stringi, tidyr, utils |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2017-06-30 |
| Author: | Mohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Nima Nouri [ctb], Steven Kleinstein [aut, cph] |
| Maintainer: | Jason Vander Heiden <jason.vanderheiden at yale.edu> |
| BugReports: | https://bitbucket.org/kleinstein/shazam/issues |
| License: | CC BY-SA 4.0 |
| 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 SHM targeting models |
| Package source: | shazam_0.1.8.tar.gz |
| Windows binaries: | r-devel: shazam_0.1.8.zip, r-release: shazam_0.1.8.zip, r-oldrel: shazam_0.1.8.zip |
| OS X El Capitan binaries: | r-release: shazam_0.1.8.tgz |
| OS X Mavericks binaries: | r-oldrel: shazam_0.1.8.tgz |
| Old sources: | shazam archive |
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