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>.
Version: 1.3.0 Depends: R (≥ 4.0), ggplot2 (≥ 3.4.0) Imports: airr (≥ 1.4.1), ape, dplyr (≥ 1.0), graphics, grid, igraph (≥ 1.5.0), Matrix (≥ 1.3-0), methods, progress, Rcpp (≥ 0.12.12), readr, rlang, scales, seqinr, stats, stringi, tibble, tidyr (≥ 1.0), utils, Biostrings (≥ 2.56.0), GenomicAlignments (≥ 1.24.0), IRanges (≥ 2.22.2) LinkingTo: Rcpp Suggests: knitr, rmarkdown, testthat Published: 2023-09-30 DOI: 10.32614/CRAN.package.alakazam Author: 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] Maintainer: Susanna Marquez <susanna.marquez at yale.edu> BugReports: https://bitbucket.org/kleinstein/alakazam/issues License: AGPL-3 URL: https://alakazam.readthedocs.io/ NeedsCompilation: yes Citation: alakazam citation info Materials: README NEWS In views: Omics CRAN checks: alakazam results Documentation: Downloads: Reverse dependencies: Linking:Please use the canonical form https://CRAN.R-project.org/package=alakazam to link to this page.
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