Package: alakazam 1.5.0.999

Susanna Marquez

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 [aut], Gisela Gabernet [ctb], Caroline Sullivan [ctb], Hailong Meng [ctb], Huimin Lyu [ctb], Burhan Sabuwala [ctb], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph]

alakazam_1.5.0.999.tar.gz
alakazam_1.5.0.999.zip(r-4.7-x86_64)alakazam_1.5.0.999.zip(r-4.7-arm64)alakazam_1.5.0.999.zip(r-4.6-x86_64)alakazam_1.5.0.999.zip(r-4.6-arm64)alakazam_1.5.0.999.zip(r-4.5-x86_64)
alakazam_1.5.0.999.tgz(r-4.6-x86_64)alakazam_1.5.0.999.tgz(r-4.6-arm64)alakazam_1.5.0.999.tgz(r-4.5-x86_64)alakazam_1.5.0.999.tgz(r-4.5-arm64)
alakazam_1.5.0.999.tar.gz(r-4.7-arm64)alakazam_1.5.0.999.tar.gz(r-4.7-x86_64)alakazam_1.5.0.999.tar.gz(r-4.6-arm64)alakazam_1.5.0.999.tar.gz(r-4.6-x86_64)
alakazam_1.5.0.999.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
alakazam/json (API)

# Install 'alakazam' in R:
install.packages('alakazam', repos = c('https://immcantation.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:

Conda:

softwareannotationdatacpp

11.77 score 3 stars 9 packages 852 scripts 2.5k downloads 6 mentions 85 exports 76 dependencies

Last updated from:bbc35ba998. Checks:13 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64WARNING239
linux-devel-x86_64WARNING237
source / vignettesOK331
linux-release-arm64WARNING263
linux-release-x86_64WARNING260
macos-release-arm64WARNING173
macos-release-x86_64WARNING527
macos-oldrel-arm64WARNING167
macos-oldrel-x86_64WARNING463
windows-devel-arm64WARNING479
windows-devel-x86_64WARNING314
windows-release-arm64WARNING478
windows-release-x86_64WARNING251
windows-oldrel-x86_64WARNING226
wasm-releaseOK151

Exports:ABBREV_AAaliphaticalphaDiversityaminoAcidPropertiesbaseThemebuildPhylipLineagebulkcalcCoveragecalcDiversitychargecheckColumnscollapseDuplicatescombineIgphymlcountClonescountGenescountPatternscpuCountDNA_COLORSDNA_IUPACestimateAbundanceextractVRegionfastDistfastDistAAgetAAMatrixgetAllelegetChaingetDNAMatrixgetFamilygetGenegetLocusgetMRCAgetPathLengthsgetPositionQualitygetSegmentgraphToPhylogravygridPlotgroupGenesIG_COLORSIMGT_REGIONSisValidAASeqIUPAC_AAIUPAC_DNAjunctionAlignmentmakeChangeoClonemakeTempDirmaskPositionsByQualitymaskSeqEndsmaskSeqGapsnonsquareDistpadSeqEndspairwiseDistpairwiseEqualpermuteLabelsphyloToGraphplotplotAbundanceCurveplotDiversityCurveplotDiversityTestplotEdgeTestplotMRCATestplotSubtreespolarprintprogressBarrarefyDiversityreadChangeoDbreadFastqDbreadIgphymlseqDistseqEqualseqMismatchCountseqMismatchMatrixseqMismatchPositionssortGenesstoufferMetasummarizeSubtreestableEdgestestDiversitytestEdgestestMRCATR_COLORStranslateDNAtranslateStringswriteChangeoDb

Dependencies:ade4airrapeBHBiocGenericsBiocParallelBiostringsbitbit64bitopscigarilloclicliprcodetoolscpp11crayondigestdplyrfarverformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehmsigraphIRangesisobandjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixnlmepillarpixmappkgconfigprettyunitsprogresspurrrR6RColorBrewerRcppRcppArmadilloreadrRhtslibrlangRsamtoolsS4VectorsS7scalessegmentedSeqinfoseqinrsnowspstringistringrtibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrXVectoryaml

Alakazam: Using sequencing quality scores
Example data | Load quality scores | Mask low quality positions
Rendered fromFastq-Vignette.Rmdusingknitr::rmarkdown

Last update: 2026-09-28
Started: 2020-11-13

Alakazam: Analysis of clonal abundance and diversity
Example data | Generate a clonal abundance curve | Generate a diversity curve | View diversity tests at a fixed diversity order
Rendered fromDiversity-Vignette.Rmdusingknitr::rmarkdown

Last update: 2026-04-28
Started: 2014-09-30

Alakazam: Amino acid physicochemical property analysis
Example data | Calculate the properties of amino acid sequences | Obtaining properties individually | Using user defined scales | Getting vectors of individual properties | Default scales
Rendered fromAminoAcids-Vignette.Rmdusingknitr::rmarkdown

Last update: 2025-12-15
Started: 2015-12-18

Alakazam: Gene usage analysis
Example data | Tabulate V(D)J allele, gene or family usage by sample | Tabulating gene abundance using additional groupings
Rendered fromGeneUsage-Vignette.Rmdusingknitr::rmarkdown

Last update: 2025-02-24
Started: 2017-05-01

Alakazam: How to read and write files
Reading data | Writing data
Rendered fromFiles-Vignette.Rmdusingknitr::rmarkdown

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