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.

Maintainer: Jason Vander Heiden <jason.vanderheiden at yale.edu>

Author(s): Mohamed Uduman*, Gur Yaari*, Namita Gupta*, Jason Vander Heiden*, Ang Cui*, Susanna Marquez*, Julian Zhou*, Steven Kleinstein*

Install package and any missing dependencies by running this line in your R console:

install.packages("shazam")

Depends R (>= 3.1.2), ggplot2(>=2.0.0)
Imports alakazam(>=0.2.4), ape, data.table(>=1.9.4), doParallel, dplyr, foreach, graphics, grid, igraph, iterators, methods, lazyeval, parallel, SDMTools, scales, seqinr, stats, stringi, tidyr, utils
Suggests knitr, rmarkdown, testthat
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Package shazam
Materials
URL http://shazam.readthedocs.io
Task Views
Version 0.1.4
Published 2016-08-06
License CC BY-NC-SA 4.0
BugReports https://bitbucket.org/kleinstein/shazam/issues
SystemRequirements
NeedsCompilation no
Citation
CRAN checks shazam check results
Package source shazam_0.1.4.tar.gz