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: 1.3.0
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:

Reference manual: alakazam.pdf
Vignettes: Amino acid property analysis
Diversity analysis
Fastq
File input and output
Gene usage analysis
Lineage reconstruction
Topology analysis

Downloads:

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 dependencies:

Reverse imports: dowser, ogrdbstats, scoper, shazam, tigger, UniprotR

Linking:

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