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>.

Package details

AuthorMohamed 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]
MaintainerJason Vander Heiden <[email protected]>
LicenseCC BY-SA 4.0
Package repositoryView on CRAN
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shazam documentation built on Sept. 21, 2018, 6:24 p.m.