shazam: Immunoglobulin Somatic Hypermutation Analysis

Share:

Provides a computational framework for Bayesian estimation of antigen-driven selection in immunoglobulin (Ig) sequences, providing an intuitive means of analyzing selection by quantifying the degree of selective pressure. Also provides tools to profile mutations in Ig sequences, build models of somatic hypermutation (SHM) in Ig sequences, and make model-dependent distance comparisons of Ig repertoires.

Author
Mohamed Uduman [aut], Gur Yaari [aut], Namita Gupta [aut], Jason Vander Heiden [aut, cre], Ang Cui [ctb], Susanna Marquez [ctb], Julian Zhou [ctb], Steven Kleinstein [aut, cph]
Date of publication
2016-08-06 01:06:04
Maintainer
Jason Vander Heiden <jason.vanderheiden@yale.edu>
License
CC BY-NC-SA 4.0
Version
0.1.4
URLs

View on CRAN

Man pages

Baseline-class
S4 class defining a BASELINe (selection) object
calcBaseline
Calculate the BASELINe PDFs
calcExpectedMutations
Calculate expected mutation frequencies of a sequence
calcObservedMutations
Count the number of observed mutations in a sequence.
calcTargetingDistance
Calculates a 5-mer distance matrix from a TargetingModel...
clearConsole
Clears the console
collapseClones
Constructs effective clonal sequences
createBaseline
Creates a Baseline object
createMutabilityMatrix
Builds a mutability model
createMutationDefinition
Creates a MutationDefinition
createRegionDefinition
Creates a RegionDefinition
createSubstitutionMatrix
Builds a substitution model
createTargetingMatrix
Calculates a targeting rate matrix
createTargetingModel
Creates a TargetingModel
distToNearest
Distance to nearest neighbor
expectedMutations
Calculate expected mutation frequencies
extendMutabilityMatrix
Extends a mutability model to include Ns.
extendSubstitutionMatrix
Extends a substitution model to include Ns.
getBaselineStats
Gets the summary statistics of a Baseline object
getnproc
Determines the numbers of CPU cores available
getPlatform
Determines the OS platform being used
groupBaseline
Group BASELINe PDFs
HS1FDistance
Human single nucleotide distance matrix.
HS5FModel
Human 5-mer targeting model.
IMGT_SCHEMES
IMGT unique numbering schemes
M1NDistance
Mouse single nucleotide distance matrix.
MRS5NFModel
Mouse 5-mer targeting model.
MutationDefinition-class
S4 class defining replacement and silent mutation definitions
MUTATION_SCHEMES
Amino acid mutation definitions
observedMutations
Calculate observed numbers of mutations
plotBaselineDensity
Plots BASELINe probability density functions
plotBaselineSummary
Plots BASELINe summary statistics
plotMutability
Plot mutability probabilities
RegionDefinition-class
S4 class defining a region definition
shazam
The shazam package
shmulateSeq
Simulate mutations in a single sequence
shmulateTree
Simulate mutations in a lineage tree
summarizeBaseline
Calculate BASELINe summary statistics
TargetingModel-class
S4 class defining a targeting model
testBaseline
Two-sided test of BASELINe PDFs
U5NModel
Uniform 5-mer targeting model.
writeTargetingDistance
Write targeting model distances to a file

Files in this package

shazam
shazam/inst
shazam/inst/CITATION
shazam/inst/doc
shazam/inst/doc/Baseline-Vignette.R
shazam/inst/doc/DistToNearest-Vignette.pdf
shazam/inst/doc/Baseline-Vignette.pdf
shazam/inst/doc/DistToNearest-Vignette.Rmd
shazam/inst/doc/Targeting-Vignette.Rmd
shazam/inst/doc/DistToNearest-Vignette.R
shazam/inst/doc/Targeting-Vignette.R
shazam/inst/doc/Targeting-Vignette.pdf
shazam/inst/doc/Baseline-Vignette.Rmd
shazam/inst/markr
shazam/inst/markr/build.R
shazam/NAMESPACE
shazam/NEWS.md
shazam/data
shazam/data/VOLUME_MUTATIONS.rda
shazam/data/HYDROPATHY_MUTATIONS.rda
shazam/data/CHARGE_MUTATIONS.rda
shazam/data/POLARITY_MUTATIONS.rda
shazam/data/M1NDistance.rda
shazam/data/IMGT_V_BY_REGIONS.rda
shazam/data/MRS5NFModel.rda
shazam/data/IMGT_V_NO_CDR3.rda
shazam/data/IMGT_V.rda
shazam/data/HS5FModel.rda
shazam/data/U5NModel.rda
shazam/data/IMGT_V_BY_REGIONS_NO_CDR3.rda
shazam/data/HS1FDistance.rda
shazam/R
shazam/R/DistToNearest.R
shazam/R/Core.R
shazam/R/Shmulate.R
shazam/R/sysdata.rda
shazam/R/Baseline.R
shazam/R/Shazam.R
shazam/R/TargetingModels.R
shazam/R/RegionDefinitions.R
shazam/R/MutationDefinitions.R
shazam/R/MutationProfiling.R
shazam/vignettes
shazam/vignettes/DistToNearest-Vignette.Rmd
shazam/vignettes/Targeting-Vignette.Rmd
shazam/vignettes/Baseline-Vignette.Rmd
shazam/README.md
shazam/MD5
shazam/build
shazam/build/vignette.rds
shazam/DESCRIPTION
shazam/man
shazam/man/MRS5NFModel.Rd
shazam/man/clearConsole.Rd
shazam/man/Baseline-class.Rd
shazam/man/shmulateTree.Rd
shazam/man/TargetingModel-class.Rd
shazam/man/createMutationDefinition.Rd
shazam/man/calcExpectedMutations.Rd
shazam/man/plotMutability.Rd
shazam/man/HS5FModel.Rd
shazam/man/shazam.Rd
shazam/man/RegionDefinition-class.Rd
shazam/man/summarizeBaseline.Rd
shazam/man/calcBaseline.Rd
shazam/man/plotBaselineDensity.Rd
shazam/man/createBaseline.Rd
shazam/man/IMGT_SCHEMES.Rd
shazam/man/getnproc.Rd
shazam/man/testBaseline.Rd
shazam/man/createTargetingMatrix.Rd
shazam/man/MUTATION_SCHEMES.Rd
shazam/man/groupBaseline.Rd
shazam/man/MutationDefinition-class.Rd
shazam/man/expectedMutations.Rd
shazam/man/U5NModel.Rd
shazam/man/extendSubstitutionMatrix.Rd
shazam/man/calcObservedMutations.Rd
shazam/man/writeTargetingDistance.Rd
shazam/man/observedMutations.Rd
shazam/man/collapseClones.Rd
shazam/man/getPlatform.Rd
shazam/man/createMutabilityMatrix.Rd
shazam/man/getBaselineStats.Rd
shazam/man/createSubstitutionMatrix.Rd
shazam/man/calcTargetingDistance.Rd
shazam/man/createRegionDefinition.Rd
shazam/man/plotBaselineSummary.Rd
shazam/man/extendMutabilityMatrix.Rd
shazam/man/HS1FDistance.Rd
shazam/man/createTargetingModel.Rd
shazam/man/shmulateSeq.Rd
shazam/man/M1NDistance.Rd
shazam/man/distToNearest.Rd