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>.

Version: 1.2.0
Depends: R (≥ 4.0), ggplot2 (≥ 3.4.0)
Imports: alakazam (≥ 1.3.0), ape, diptest, doParallel, dplyr (≥ 1.0), foreach, graphics, grid, igraph (≥ 1.5.0), iterators, KernSmooth, lazyeval, MASS, methods, parallel, progress, rlang, scales, seqinr, stats, stringi (≥ 1.1.3), tidyr, tidyselect, utils
Suggests: knitr, rmarkdown, testthat
Published: 2023-10-02
Author: Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut, cre], Julian Zhou [aut], Nima Nouri [aut], Noah Yann Lee [aut], Ang Cui [ctb], Jason Vander Heiden [aut], Gur Yaari [aut], Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez at yale.edu>
BugReports: https://bitbucket.org/kleinstein/shazam/issues
License: AGPL-3
URL: http://shazam.readthedocs.io
NeedsCompilation: no
Citation: shazam citation info
Materials: README NEWS
CRAN checks: shazam results

Documentation:

Reference manual: shazam.pdf
Vignettes: Selection quantification
Distance to nearest neighbor
Mutation analysis
Simulating sequence mutations
SHM targeting models

Downloads:

Package source: shazam_1.2.0.tar.gz
Windows binaries: r-devel: shazam_1.2.0.zip, r-release: shazam_1.2.0.zip, r-oldrel: shazam_1.2.0.zip
macOS binaries: r-release (arm64): shazam_1.2.0.tgz, r-oldrel (arm64): shazam_1.2.0.tgz, r-release (x86_64): shazam_1.2.0.tgz
Old sources: shazam archive

Reverse dependencies:

Reverse imports: dowser, scoper

Linking:

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