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], Namita Gupta [aut], Susanna Marquez [aut], Julian Zhou [aut], Nima Nouri [aut], Ang Cui [ctb], Jason Vander Heiden [aut, cre], Gur Yaari [aut], Steven Kleinstein [aut, cph]
MaintainerJason Vander Heiden <jason.vanderheiden@gmail.com>
LicenseAGPL-3
Version1.1.0
URL http://shazam.readthedocs.io
Package repositoryView on CRAN
Installation Install the latest version of this package by entering the following in R:
install.packages("shazam")

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shazam documentation built on July 9, 2021, 1:07 a.m.