shazam

MaRDI QIDQ28011swMATHCRANFDO

Authors 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

Description

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>.

Cites work

• 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