shazam
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SHazaM
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Installing Released Versions
Building Development Versions
Package Overview
Release Notes
Version 1.2.0: October 10, 2023
Version 1.1.2: September 26, 2022
Version 1.1.1: May 23, 2022
Version 1.1.0: July 8, 2021
Version 1.0.2: August 10, 2020
Version 1.0.1: July 18, 2020
Version 1.0.0 May 9, 2020
Version 0.2.3 February 5, 2020
Version 0.2.2 December 15, 2019
Version 0.2.1 July 19, 2019
Version 0.2.0 July 18, 2019
Version 0.1.11: January 27, 2019
Version 0.1.10: September 19, 2018
Version 0.1.9: March 30, 2018
Version 0.1.8: June 30, 2017
Version 0.1.7: May 14, 2017
Version 0.1.6: May 12, 2017
Version 0.1.5: March 23, 2017
Version 0.1.4: August 5, 2016
Version 0.1.3: July 31, 2016
Version 0.1.2: February 20, 2016
Version 0.1.1: December 18, 2015
Version 0.1.0: June 18, 2015
Version 0.1.0.beta-2015-05-30: May 30, 2015
Version 0.1.0.beta-2015-05-11: May 11, 2015
Version 0.1.0.beta-2015-05-05: May 05, 2015
Related Projects
Vignettes
Basic mutational load analysis
Example data
Calculate the counts and frequencies of mutations over the entire sequence
Calculate mutations within subregions
Use amino acid physicochemical properties to define mutations
Quantification of selection pressure
Example data
Preprocessing
Calculate selection PDFs for individual sequences
Group and convolve individual selection distributions
Plot and compare selection scores for groups
Editing a field in a Baseline object
Tuning clonal assignment thresholds with nearest neighbor distances
Example data
Calculating nearest neighbor distances (heavy chain sequences)
Calculating nearest neighbor distances (single-cell paired heavy and light chain sequences)
Using nearest neighbor distances to determine clonal assignment thresholds
Calculating nearest neighbor distances independently for subsets of data
Calculating nearest neighbor distances across groups rather than within a groups
Speeding up pairwise-distance-matrix calculations with subsampling
Inferring SHM targeting models
Example data
Infer targeting model (substitution and mutability)
Visualize targeting model
Calculate targeting distance matrix
Simulation based on a targeting model
Simulate mutations in a single sequence
Simulate mutations in a lineage tree
Help Topics
Mutation Profiling
collapseClones
consensusSequence
expectedMutations
observedMutations
calcExpectedMutations
calcObservedMutations
slideWindowDb
slideWindowSeq
slideWindowTune
slideWindowTunePlot
plotSlideWindowTune
shmulateSeq
shmulateTree
Targeting Inference
calculateMutability
createMutabilityMatrix
createSubstitutionMatrix
extendMutabilityMatrix
extendSubstitutionMatrix
createTargetingMatrix
createTargetingModel
makeAverage1merMut
makeAverage1merSub
makeDegenerate5merMut
makeDegenerate5merSub
minNumMutationsTune
minNumSeqMutationsTune
plotMutability
plotTune
MutabilityModel class
TargetingMatrix class
TargetingModel class
Empirical Models
HH S1F
HH S5F
HKL S1F
HKL S5F
MK RS1NF
MK RS5NF
U5N
Selection Analysis
calcBaseline
groupBaseline
summarizeBaseline
testBaseline
makeGraphDf
plotBaselineDensity
plotBaselineSummary
createBaseline
editBaseline
Baseline class
Distance Profiling
distToNearest
findThreshold
plotDensityThreshold
plotGmmThreshold
calcTargetingDistance
writeTargetingDistance
DensityThreshold class
GmmThreshold class
Mutation & Region Definitions
MUTATION SCHEMES
IMGT SCHEMES
createMutationDefinition
createRegionDefinition
setRegionBoundaries
MutationDefinition class
RegionDefinition class
convertNumbering
shazam
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