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

On CRAN:

51 exports 1.89 score 102 dependencies 2 dependents 206 scripts 691 downloads

Last updated 2 months agofrom:ce27e4098f. Checks:OK: 1 WARNING: 6. Indexed: yes.

Exports:as.data.framecalcBaselinecalcExpectedMutationscalcObservedMutationscalcTargetingDistancecalculateMutabilitycollapseClonesconsensusSequenceconvertNumberingcreateBaselinecreateMutabilityMatrixcreateMutationDefinitioncreateRegionDefinitioncreateSubstitutionMatrixcreateTargetingMatrixcreateTargetingModeldistToNearesteditBaselineexpectedMutationsextendMutabilityMatrixextendSubstitutionMatrixfindThresholdgroupBaselinemakeAverage1merMutmakeAverage1merSubmakeDegenerate5merMutmakeDegenerate5merSubmakeGraphDfminNumMutationsTuneminNumSeqMutationsTuneobservedMutationsplotplotBaselineDensityplotBaselineSummaryplotDensityThresholdplotGmmThresholdplotMutabilityplotSlideWindowTuneplotTuneprintsetRegionBoundariesshmulateSeqshmulateTreeslideWindowDbslideWindowSeqslideWindowTuneslideWindowTunePlotsummarizeBaselinesummarytestBaselinewriteTargetingDistance

Dependencies:abindade4airralakazamapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdiptestdoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryamlzlibbioc