shazam
swMATH16140CRANshazamMaRDI QIDQ28011FDOQ28011
Immunoglobulin Somatic Hypermutation Analysis
Mohamed Uduman, Susanna Marquez, Nima Nouri, Noah Yann Lee, Julian Zhou, Namita Gupta, Gur Yaari, Steven H. Kleinstein, Jason A. vander Heiden
Last update: 2 October 2023
Copyright license: GNU Affero General Public License, version 3.0
Software version identifier: 1.1.2, 0.1.2, 0.1.3, 0.1.4, 0.1.5, 0.1.6, 0.1.7, 0.1.8, 0.1.9, 0.1.10, 0.1.11, 0.2.0, 0.2.1, 0.2.2, 0.2.3, 1.0.0, 1.0.1, 1.0.2, 1.1.0, 1.1.1, 1.2.0
Official website: https://cran.r-project.org/package=shazam
Source code repository: https://github.com/cran/shazam
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>.
- Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data
- Quantifying selection in high-throughput Immunoglobulin sequencing data sets
- Models of Somatic Hypermutation Targeting and Substitution Based on Synonymous Mutations from High-Throughput Immunoglobulin Sequencing Data
- A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data
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