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'))

Peer review:

Bug tracker:https://bitbucket.org/kleinstein/shazam

Datasets:

    On CRAN:

    7.48 score 2 packages 224 scripts 675 downloads 51 exports 102 dependencies

    Last updated 19 days agofrom:563e3b6d89. Checks:OK: 1 WARNING: 6. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKNov 04 2024
    R-4.5-winWARNINGNov 04 2024
    R-4.5-linuxWARNINGNov 04 2024
    R-4.4-winWARNINGNov 04 2024
    R-4.4-macWARNINGNov 04 2024
    R-4.3-winWARNINGNov 04 2024
    R-4.3-macWARNINGOct 04 2024

    Exports:as.data.framecalcBaselinecalcExpectedMutationscalcObservedMutationscalcTargetingDistancecalculateMutabilitycollapseClonesconsensusSequenceconvertNumberingcreateBaselinecreateMutabilityMatrixcreateMutationDefinitioncreateRegionDefinitioncreateSubstitutionMatrixcreateTargetingMatrixcreateTargetingModeldistToNearesteditBaselineexpectedMutationsextendMutabilityMatrixextendSubstitutionMatrixfindThresholdgroupBaselinemakeAverage1merMutmakeAverage1merSubmakeDegenerate5merMutmakeDegenerate5merSubmakeGraphDfminNumMutationsTuneminNumSeqMutationsTuneobservedMutationsplotplotBaselineDensityplotBaselineSummaryplotDensityThresholdplotGmmThresholdplotMutabilityplotSlideWindowTuneplotTuneprintsetRegionBoundariesshmulateSeqshmulateTreeslideWindowDbslideWindowSeqslideWindowTuneslideWindowTunePlotsummarizeBaselinesummarytestBaselinewriteTargetingDistance

    Dependencies:abindade4airralakazamapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdiptestdoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryamlzlibbioc

    Shazam: Tuning clonal assignment thresholds with nearest neighbor distances

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

    Rendered fromDistToNearest-Vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

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

    Shazam: Mutation analysis

    Susanna Marquez & Julian Q. Zhou

    Rendered fromMutation-Vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

    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 Nov 04 2024.

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

    Shazam: Inferring SHM targeting models

    Namita Gupta & Julian Q. Zhou

    Rendered fromTargeting-Vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

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

    Shazam: Simulating sequence mutations

    Julian Q. Zhou

    Rendered fromShmulate-Vignette.Rmdusingknitr::rmarkdownon Nov 04 2024.

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