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
Cited In (13)
- Spurious Regressions with Time-Series Data: Further Asymptotic Results
- A fuzzy logic approach to modelling the New Zealand underground economy
- SoDA2
- DeepTCR
- Ace
- Alakazam
- Change-O
- OLGA
- repgenHMM
- dowser
- scoper
- Quantitative immunology for physicists
- Bounds on the effect of heteroscedasticity on the chow test for structural change
This page was built for software: shazam
