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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:

Please use the canonical form https://CRAN.R-project.org/package=alakazam to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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