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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 |
| 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 |
| Reference manual: | alakazam.pdf |
| Vignettes: |
Amino acid property analysis Diversity analysis Fastq File input and output Gene usage analysis Lineage reconstruction Topology analysis |
| Package source: | alakazam_1.3.0.tar.gz |
| Windows binaries: | r-devel: alakazam_1.3.0.zip, r-release: alakazam_1.3.0.zip, r-oldrel: alakazam_1.3.0.zip |
| macOS binaries: | r-release (arm64): alakazam_1.3.0.tgz, r-oldrel (arm64): alakazam_1.3.0.tgz, r-release (x86_64): alakazam_1.3.0.tgz, r-oldrel (x86_64): alakazam_1.3.0.tgz |
| Old sources: | alakazam archive |
| Reverse imports: | dowser, ogrdbstats, scoper, shazam, tigger, UniprotR |
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