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: | 1.4.2 |
| 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: | 2025-12-16 |
| 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 [aut], Gisela Gabernet [ctb], Caroline Sullivan [ctb], Hailong Meng [ctb], Huimin Lyu [ctb], Burhan Sabuwala [ctb], Jason Vander Heiden [aut], Steven Kleinstein [aut, cph] |
| Maintainer: | Susanna Marquez <susanna.marquez at yale.edu> |
| BugReports: | https://github.com/immcantation/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 |
| Reference manual: | alakazam.html ,alakazam.pdf |
| Vignettes: | Amino acid property analysis (source,R code) Diversity analysis (source,R code) Fastq (source,R code) File input and output (source,R code) Gene usage analysis (source,R code) |
| Package source: | alakazam_1.4.2.tar.gz |
| Windows binaries: | r-devel:alakazam_1.4.2.zip, r-release:alakazam_1.4.1.zip, r-oldrel:alakazam_1.4.2.zip |
| macOS binaries: | r-release (arm64):alakazam_1.4.2.tgz, r-oldrel (arm64):alakazam_1.4.2.tgz, r-release (x86_64):alakazam_1.4.2.tgz, r-oldrel (x86_64):alakazam_1.4.2.tgz |
| Old sources: | alakazam archive |
| Reverse imports: | dowser,ogrdbstats,scoper,shazam,tigger,UniprotR |
| Reverse suggests: | AntibodyForests |
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