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: | 0.2.11 |
| Depends: | R (≥ 3.1.2), ggplot2 (≥ 2.0.0) |
| Imports: | dplyr (≥ 0.5.0), graphics, grid, igraph (≥ 1.0.0), lazyeval, methods, progress, Rcpp (≥ 0.12.12), readr, scales, seqinr, stats, stringi, tidyr, utils |
| LinkingTo: | Rcpp |
| Suggests: | knitr, rmarkdown, testthat |
| Published: | 2018-09-14 |
| Author: | Jason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Ruoyi Jiang [ctb], Nima Nouri [ctb], Steven Kleinstein [aut, cph] |
| Maintainer: | Jason Vander Heiden <jason.vanderheiden at yale.edu> |
| BugReports: | https://bitbucket.org/kleinstein/alakazam/issues |
| License: | CC BY-SA 4.0 |
| URL: | http://alakazam.readthedocs.org |
| NeedsCompilation: | yes |
| SystemRequirements: | C++11 |
| Citation: | alakazam citation info |
| Materials: | README NEWS |
| CRAN checks: | alakazam results |
| Reference manual: | alakazam.pdf |
| Vignettes: |
Amino acid property analysis Diversity analysis Gene usage analysis Lineage reconstruction Topology analysis |
| Package source: | alakazam_0.2.11.tar.gz |
| Windows binaries: | r-devel: alakazam_0.2.11.zip, r-release: alakazam_0.2.11.zip, r-oldrel: alakazam_0.2.11.zip |
| OS X binaries: | r-release: alakazam_0.2.11.tgz, r-oldrel: alakazam_0.2.11.tgz |
| Old sources: | alakazam archive |
| Reverse imports: | rabhit, scoper, shazam, tigger |
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