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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", "1.2.0")



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: 2022-10-01
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 1.2.0, https://cran.r-project.org/web/packages/shazam
Previous versions and publish date:
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)
Other packages that cited shazam R package
View shazam citation profile
Other R packages that shazam depends, imports, suggests or enhances
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
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