Package: shazam
Type: Package
Version: 0.1.9
Date: 2018-03-30
Authors@R: c(person("Mohamed", "Uduman", role=c("aut"), 
                    email="mohamed.uduman@yale.edu"),
             person("Gur", "Yaari", role=c("aut"), 
                    email="gur.yaari@biu.ac.il"),
             person("Namita", "Gupta", role=c("aut"), 
                    email="namita.gupta@yale.edu"),
             person("Jason", "Vander Heiden", role=c("aut", "cre"), 
                    email="jason.vanderheiden@yale.edu"),
             person("Ang", "Cui", role=c("ctb"), 
                    email="angcui@mit.edu"),
             person("Susanna", "Marquez", role=c("ctb"), 
                    email="susanna.marquez@yale.edu"),
             person("Julian", "Zhou", role=c("ctb"), 
                    email="julian.zhou@yale.edu"),
             person("Nima", "Nouri", role=c("ctb"), 
                    email="nima.nouri@yale.edu"),
             person("Steven", "Kleinstein", role=c("aut", "cph"), 
                    email="steven.kleinstein@yale.edu"))
Title: Immunoglobulin Somatic Hypermutation Analysis
Description: 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.
    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>.
License: CC BY-SA 4.0
URL: http://shazam.readthedocs.io
BugReports: https://bitbucket.org/kleinstein/shazam/issues
LazyData: true
BuildVignettes: true
VignetteBuilder: knitr
Depends: R (>= 3.1.2), ggplot2 (>= 2.0.0), stringi (>= 1.1.3)
Imports: alakazam (>= 0.2.10), ape, diptest, doParallel, dplyr (>=
        0.5.0), foreach, graphics, grid, igraph, iterators, kedd,
        KernSmooth, lazyeval, MASS, methods, parallel, progress,
        SDMTools, scales, seqinr, stats, tidyr, utils
Suggests: knitr, rmarkdown, testthat
Collate: 'Shazam.R' 'RegionDefinitions.R' 'Baseline.R' 'Core.R'
        'DistToNearest.R' 'MutationDefinitions.R' 'MutationProfiling.R'
        'Shmulate.R' 'TargetingModels.R'
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-03-30 15:42:12 UTC; jason
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@yale.edu>
Repository: CRAN
Date/Publication: 2018-03-31 22:32:38 UTC
Built: R 3.3.3; ; 2018-04-22 17:53:21 UTC; windows
