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

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

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

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

On CRAN:

softwareannotationdatacpp

9.09 score 7 packages 424 scripts 1.3k downloads 6 mentions 80 exports 94 dependencies

Last updated 2 months agofrom:b1214190aa. Checks:1 OK, 9 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-win-x86_64WARNINGFeb 17 2025
R-4.5-mac-x86_64WARNINGFeb 17 2025
R-4.5-mac-aarch64WARNINGFeb 17 2025
R-4.5-linux-x86_64WARNINGFeb 17 2025
R-4.4-win-x86_64WARNINGFeb 17 2025
R-4.4-mac-x86_64WARNINGFeb 17 2025
R-4.4-mac-aarch64WARNINGFeb 17 2025
R-4.3-win-x86_64WARNINGFeb 17 2025
R-4.3-mac-x86_64WARNINGFeb 17 2025

Exports:ABBREV_AAaliphaticalphaDiversityaminoAcidPropertiesbaseThemebuildPhylipLineagebulkcalcCoveragecalcDiversitychargecheckColumnscollapseDuplicatescombineIgphymlcountClonescountGenescountPatternscpuCountDNA_COLORSDNA_IUPACestimateAbundanceextractVRegiongetAAMatrixgetAllelegetChaingetDNAMatrixgetFamilygetGenegetLocusgetMRCAgetPathLengthsgetPositionQualitygetSegmentgraphToPhylogravygridPlotgroupGenesIG_COLORSIMGT_REGIONSisValidAASeqIUPAC_AAIUPAC_DNAjunctionAlignmentmakeChangeoClonemakeTempDirmaskPositionsByQualitymaskSeqEndsmaskSeqGapsnonsquareDistpadSeqEndspairwiseDistpairwiseEqualpermuteLabelsphyloToGraphplotplotAbundanceCurveplotDiversityCurveplotDiversityTestplotEdgeTestplotMRCATestplotSubtreespolarprintprogressBarrarefyDiversityreadChangeoDbreadFastqDbreadIgphymlseqDistseqEqualsortGenesstoufferMetasummarizeSubtreestableEdgestestDiversitytestEdgestestMRCATR_COLORStranslateDNAtranslateStringswriteChangeoDb

Dependencies:abindade4airrapeaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsclicliprcodetoolscolorspacecpp11crayoncurlDelayedArraydigestdplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehmshttrigraphIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4ArraysS4VectorsscalessegmentedseqinrsnowspSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectoryaml

Alakazam: Amino acid physicochemical property analysis

Susanna Marquez

Rendered fromAminoAcids-Vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

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 Feb 17 2025.

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

Alakazam: Using sequencing quality scores

Susanna Marquez

Rendered fromFastq-Vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

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

Alakazam: How to read and write files

Edel Aron

Rendered fromFiles-Vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

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

Alakazam: Gene usage analysis

Susanna Marquez

Rendered fromGeneUsage-Vignette.Rmdusingknitr::rmarkdownon Feb 17 2025.

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