shazam

Immunoglobulin Somatic Hypermutation Analysis

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>.

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Description file content

Package
shazam
Type
Package
Version
0.2.1
Date
2019-07-19
Title
Immunoglobulin Somatic Hypermutation Analysis
Description
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) , Yaari, et al (2012) , Yaari, et al (2013) , Cui, et al (2016) .
License
CC BY-SA 4.0
URL
BugReports
https://bitbucket.org/kleinstein/shazam/issues
LazyData
true
BuildVignettes
true
VignetteBuilder
knitr
Encoding
UTF-8
Depends
R (>= 3.1.2), ggplot2 (>= 2.0.0), stringi (>= 1.1.3)
Imports
alakazam (>= 0.3.0), ape, diptest, doParallel, dplyr (>= 0.8.1), foreach, graphics, grid, igraph, iterators, kedd, KernSmooth, lazyeval, MASS, methods, parallel, progress, rlang, 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
6.1.1
NeedsCompilation
no
Packaged
2019-07-19 18:19:10 UTC; vandej27
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
Repository
CRAN
Date/Publication
2019-07-19 22:30:02 UTC

install.packages('shazam')

0.2.1

a month ago

http://shazam.readthedocs.io

Jason Vander Heiden

CC BY-SA 4.0

Depends on

R (>= 3.1.2), ggplot2 (>= 2.0.0), stringi (>= 1.1.3)

Imports

alakazam (>= 0.3.0), ape, diptest, doParallel, dplyr (>= 0.8.1), foreach, graphics, grid, igraph, iterators, kedd, KernSmooth, lazyeval, MASS, methods, parallel, progress, rlang, SDMTools, scales, seqinr, stats, tidyr, utils

Suggests

knitr, rmarkdown, testthat

Discussions