Other packages > Find by keyword >

shazam  

Immunoglobulin Somatic Hypermutation Analysis
View on CRAN: Click here


Download and install shazam package within the R console
Install from CRAN:
install.packages("shazam")

Install from Github:
library("remotes")
install_github("cran/shazam")

Install by package version:
library("remotes")
install_version("shazam", "1.3.2")



Attach the package and use:
library("shazam")
Maintained by
Susanna Marquez
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2016-02-21
Latest Update: 2023-10-02
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) , Yaari, et al (2012) , Yaari, et al (2013) , Cui, et al (2016) .
How to cite:
Susanna Marquez (2016). shazam: Immunoglobulin Somatic Hypermutation Analysis. R package version 1.3.2, https://cran.r-project.org/web/packages/shazam. Accessed 08 Oct. 2026.
Previous versions and publish date:
(2026-10-02 00:30), 0.1.2 (2016-02-21 15:58), 0.1.3 (2016-07-31 23:20), 0.1.4 (2016-08-06 01:06), 0.1.5 (2017-03-24 07:25), 0.1.6 (2017-05-13 01:27), 0.1.7 (2017-05-14 22:44), 0.1.8 (2017-06-30 23:47), 0.1.9 (2018-04-01 00:32), 0.1.10 (2018-09-20 20:00), 0.1.11 (2019-01-28 14:10), 0.2.0 (2019-07-19 00:40), 0.2.1 (2019-07-20 00:30), 0.2.2 (2019-12-16 07:10), 0.2.3 (2020-02-06 07:20), 1.0.0 (2020-05-11 19:00), 1.0.1 (2020-07-19 18:30), 1.0.2 (2020-08-11 18:00), 1.1.0 (2021-07-09 00:00), 1.1.1 (2022-05-24 00:50), 1.1.2 (2022-10-01 09:30), 1.2.0 (2023-10-02 20:50), 1.3.0 (2025-10-20 20:30), 1.3.1 (2026-01-08 09:40), 1.3.2 (2026-05-01 09:20)
Other packages that cited shazam R package
View shazam citation profile
Other R packages that shazam depends, imports, suggests or enhances
Complete documentation for shazam
Functions, R codes and Examples using the shazam R package
Some associated functions: Baseline-class . DensityThreshold-class . GmmThreshold-class . HH_S1F . HH_S5F . HKL_S1F . HKL_S5F . IMGT_SCHEMES . MK_RS1NF . MK_RS5NF . MUTATION_SCHEMES . MutabilityModel-class . MutationDefinition-class . RegionDefinition-class . TargetingMatrix-class . TargetingModel-class . U5N . calcBaseline . calcExpectedMutations . calcObservedMutations . calcTargetingDistance . calculateMutability . collapseClones . consensusSequence . convertNumbering . createBaseline . createMutabilityMatrix . createMutationDefinition . createRegionDefinition . createSubstitutionMatrix . createTargetingMatrix . createTargetingModel . distToNearest . editBaseline . expectedMutations . extendMutabilityMatrix . extendSubstitutionMatrix . findThreshold . groupBaseline . makeAverage1merMut . makeAverage1merSub . makeDegenerate5merMut . makeDegenerate5merSub . makeGraphDf . minNumMutationsTune . minNumSeqMutationsTune . observedMutations . plotBaselineDensity . plotBaselineSummary . plotDensityThreshold . plotGmmThreshold . plotMutability . plotSlideWindowTune . plotTune . setRegionBoundaries . shazam-package . shazam . shmulateSeq . shmulateTree . slideWindowDb . slideWindowSeq . slideWindowTune . slideWindowTunePlot . summarizeBaseline . testBaseline . writeTargetingDistance . 
Some associated R codes: Baseline.R . ConvertNumbering.R . Core.R . Deprecated.R . DistToNearest.R . MutationDefinitions.R . MutationProfiling.R . RegionDefinitions.R . RegionsExtend.R . Shazam.R . Shmulate.R . TargetingModels.R . kedd.R .  Full shazam package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
kriens  
Continuation Passing Style Development
Provides basic functions for Continuation-Passing Style development. ...
Download / Learn more Package Citations See dependency  
shinymodels  
Interactive Assessments of Models
Launch a 'shiny' application for 'tidymodels' results. For classification or regression models, the ...
Download / Learn more Package Citations See dependency  
imguR  
An Imgur.com API Client Package
A complete API client for the image hosting service Imgur.com, including the an imgur graphics devic ...
Download / Learn more Package Citations See dependency  
eDMA  
Dynamic Model Averaging with Grid Search
Perform dynamic model averaging with grid search as in Dangl and Halling (2012) ...
Download / Learn more Package Citations See dependency  

28,989

R Packages

247,686

Dependencies

76,495

Author Associations

28,990

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA