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>.

Version: 1.0.1
Depends: R (≥ 3.5.0), ggplot2 (≥ 3.2.0)
Imports: ape, dplyr (≥ 0.8.3), graphics, grid, igraph (≥ 1.0.0), lazyeval, Matrix, methods, progress, Rcpp (≥ 0.12.12), readr, rlang, scales, seqinr, stats, stringi, tibble, tidyr (≥ 1.0.0), utils
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, testthat
Published: 2020-05-11
Author: Namita Gupta [aut], Susanna Marquez [aut], Nima Nouri [aut], Ruoyi Jiang [aut], Julian Zhou [aut], Kenneth Hoehn [aut], Daniel Gadala-Maria [ctb], Jason Vander Heiden [cre, aut], Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden at gmail.com>
BugReports: https://bitbucket.org/kleinstein/alakazam/issues
License: AGPL-3
URL: http://alakazam.readthedocs.org
NeedsCompilation: yes
SystemRequirements: C++11
Citation: alakazam citation info
Materials: README NEWS
CRAN checks: alakazam results

Downloads:

Reference manual: alakazam.pdf
Vignettes: Amino acid property analysis
Diversity analysis
Gene usage analysis
Lineage reconstruction
Topology analysis
Package source: alakazam_1.0.1.tar.gz
Windows binaries: r-devel: alakazam_1.0.1.zip, r-release: alakazam_1.0.1.zip, r-oldrel: alakazam_1.0.1.zip
macOS binaries: r-release: alakazam_1.0.1.tgz, r-oldrel: alakazam_1.0.1.tgz
Old sources: alakazam archive

Reverse dependencies:

Reverse imports: scoper, shazam, tigger, UniprotR

Linking:

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