shazam: Immunoglobulin Somatic Hypermutation Analysis

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: 0.1.5
Depends: R (≥ 3.1.2), ggplot2 (≥ 2.0.0)
Imports: alakazam (≥ 0.2.6), ape, data.table (≥ 1.9.4), doParallel, dplyr, foreach, graphics, grid, igraph, iterators, kedd, KernSmooth, methods, lazyeval, parallel, SDMTools, scales, seqinr, stats, stringi, tidyr, utils
Suggests: knitr, rmarkdown, testthat
Published: 2017-03-24
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

Downloads:

Reference manual: shazam.pdf
Vignettes: Selection quantification
Distance to nearest neighbor
SHM targeting models
Package source: shazam_0.1.5.tar.gz
Windows binaries: r-devel: shazam_0.1.5.zip, r-release: shazam_0.1.5.zip, r-oldrel: shazam_0.1.5.zip
OS X El Capitan binaries: r-release: shazam_0.1.5.tgz
OS X Mavericks binaries: r-oldrel: shazam_0.1.5.tgz
Old sources: shazam archive

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