Package: alakazam 1.3.1.999

alakazam: Immunoglobulin Clonal Lineage and Diversity Analysis

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

Authors:Susanna Marquez [cre, aut], Namita Gupta [aut], Nima Nouri [aut], Ruoyi Jiang [aut], Julian Zhou [aut], Kenneth Hoehn [aut], Daniel Gadala-Maria [ctb], Edel Aron [ctb], Cole Jensen [ctb], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph]

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NEWS

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

Peer review:

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

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

    On CRAN:

    80 exports 2.99 score 95 dependencies 6 dependents 6 mentions 388 scripts 1.4k downloads

    Last updated 2 months agofrom:e493319e43. Checks:OK: 1 WARNING: 8. Indexed: yes.

    TargetResultDate
    Doc / VignettesOKAug 31 2024
    R-4.5-win-x86_64WARNINGAug 31 2024
    R-4.5-linux-x86_64WARNINGAug 31 2024
    R-4.4-win-x86_64WARNINGAug 31 2024
    R-4.4-mac-x86_64WARNINGAug 31 2024
    R-4.4-mac-aarch64WARNINGAug 31 2024
    R-4.3-win-x86_64WARNINGAug 31 2024
    R-4.3-mac-x86_64WARNINGAug 31 2024
    R-4.3-mac-aarch64WARNINGAug 31 2024

    Exports:ABBREV_AAaliphaticalphaDiversityaminoAcidPropertiesbaseThemebuildPhylipLineagebulkcalcCoveragecalcDiversitychargecheckColumnscollapseDuplicatescombineIgphymlcountClonescountGenescountPatternscpuCountDNA_COLORSDNA_IUPACestimateAbundanceextractVRegiongetAAMatrixgetAllelegetChaingetDNAMatrixgetFamilygetGenegetLocusgetMRCAgetPathLengthsgetPositionQualitygetSegmentgraphToPhylogravygridPlotgroupGenesIG_COLORSIMGT_REGIONSisValidAASeqIUPAC_AAIUPAC_DNAjunctionAlignmentmakeChangeoClonemakeTempDirmaskPositionsByQualitymaskSeqEndsmaskSeqGapsnonsquareDistpadSeqEndspairwiseDistpairwiseEqualpermuteLabelsphyloToGraphplotplotAbundanceCurveplotDiversityCurveplotDiversityTestplotEdgeTestplotMRCATestplotSubtreespolarprintprogressBarrarefyDiversityreadChangeoDbreadFastqDbreadIgphymlseqDistseqEqualsortGenesstoufferMetasummarizeSubtreestableEdgestestDiversitytestEdgestestMRCATR_COLORStranslateDNAtranslateStringswriteChangeoDb

    Dependencies:abindade4airrapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryamlzlibbioc

    Alakazam: Amino acid physicochemical property analysis

    Susanna Marquez

    Rendered fromAminoAcids-Vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

    Last update: 2021-01-20
    Started: 2015-12-18

    Alakazam: Analysis of clonal abundance and diversity

    Jason Anthony Vander Heiden

    Rendered fromDiversity-Vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

    Last update: 2024-01-18
    Started: 2014-09-30

    Alakazam: Using sequencing quality scores

    Susanna Marquez

    Rendered fromFastq-Vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

    Last update: 2022-09-19
    Started: 2020-11-13

    Alakazam: How to read and write files

    Edel Aron

    Rendered fromFiles-Vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

    Last update: 2021-02-01
    Started: 2020-11-24

    Alakazam: Gene usage analysis

    Susanna Marquez

    Rendered fromGeneUsage-Vignette.Rmdusingknitr::rmarkdownon Aug 31 2024.

    Last update: 2020-12-11
    Started: 2017-05-01