Package: shazam 1.2.1.999

shazam: Immunoglobulin Somatic Hypermutation Analysis

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>.

Authors:Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut, cre], Julian Zhou [aut], Nima Nouri [aut], Noah Yann Lee [aut], Ang Cui [ctb], Jason Vander Heiden [aut], Gur Yaari [aut], Steven Kleinstein [aut, cph]

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shazam.pdf |shazam.html✨
shazam/json (API)
NEWS

# Install 'shazam' in R:
install.packages('shazam', repos = c('https://ssnn-airr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/immcantation/shazam/issues

On CRAN:

7.43 score 2 packages 222 scripts 785 downloads 51 exports 101 dependencies

Last updated 1 months agofrom:b223a25e36. Checks:1 OK, 5 WARNING, 1 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 07 2025
R-4.5-winWARNINGFeb 07 2025
R-4.5-macWARNINGFeb 07 2025
R-4.5-linuxWARNINGFeb 07 2025
R-4.4-winWARNINGFeb 07 2025
R-4.4-macWARNINGFeb 07 2025
R-4.3-winOUTDATEDDec 04 2024

Exports:as.data.framecalcBaselinecalcExpectedMutationscalcObservedMutationscalcTargetingDistancecalculateMutabilitycollapseClonesconsensusSequenceconvertNumberingcreateBaselinecreateMutabilityMatrixcreateMutationDefinitioncreateRegionDefinitioncreateSubstitutionMatrixcreateTargetingMatrixcreateTargetingModeldistToNearesteditBaselineexpectedMutationsextendMutabilityMatrixextendSubstitutionMatrixfindThresholdgroupBaselinemakeAverage1merMutmakeAverage1merSubmakeDegenerate5merMutmakeDegenerate5merSubmakeGraphDfminNumMutationsTuneminNumSeqMutationsTuneobservedMutationsplotplotBaselineDensityplotBaselineSummaryplotDensityThresholdplotGmmThresholdplotMutabilityplotSlideWindowTuneplotTuneprintsetRegionBoundariesshmulateSeqshmulateTreeslideWindowDbslideWindowSeqslideWindowTuneslideWindowTunePlotsummarizeBaselinesummarytestBaselinewriteTargetingDistance

Dependencies:abindade4airralakazamapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdiptestdoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryaml

Shazam: Tuning clonal assignment thresholds with nearest neighbor distances

Namita Gupta, Susanna Marquez, Nima Nouri and Julian Q. Zhou

Rendered fromDistToNearest-Vignette.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-04-02
Started: 2015-02-04

Shazam: Mutation analysis

Susanna Marquez & Julian Q. Zhou

Rendered fromMutation-Vignette.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2023-11-06
Started: 2017-04-03

Shazam: Quantification of selection pressure

Namita Gupta & Jason Anthony Vander Heiden & Julian Q. Zhou

Rendered fromBaseline-Vignette.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-04-02
Started: 2015-04-28

Shazam: Inferring SHM targeting models

Namita Gupta & Julian Q. Zhou

Rendered fromTargeting-Vignette.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-04-02
Started: 2015-04-25

Shazam: Simulating sequence mutations

Julian Q. Zhou

Rendered fromShmulate-Vignette.Rmdusingknitr::rmarkdownon Feb 07 2025.

Last update: 2024-04-02
Started: 2018-03-16