Alakazam

Alakazam is part of the Immcantation analysis framework for Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) and provides a set of tools to investigate lymphocyte receptor clonal lineages, diversity, gene usage, and other repertoire level properties, with a focus on high-throughput immunoglobulin (Ig) sequencing.

Alakazam serves five main purposes:

  1. Providing core functionality for other R packages in the Immcantation framework. This includes common tasks such as file I/O, basic DNA sequence manipulation, and interacting with V(D)J segment and gene annotations.
  2. Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
  3. Performing lineage reconstruction on clonal populations of Ig sequences and analyzing the topology of the resultant lineage trees.
  4. Performing clonal abundance and diversity analysis on lymphocyte repertoires.
  5. Performing physicochemical property analyses of lymphocyte receptor sequences.

Dependencies

Depends: ggplot2
Imports: dplyr, graphics, grid, igraph, lazyeval, methods, Rcpp, readr, scales, seqinr, stats, stringi, utils
Suggests: knitr, rmarkdown, testthat

Authors

Jason Vander Heiden (aut, cre)
Namita Gupta (aut)
Susanna Marquez (ctb)
Daniel Gadala-Maria (ctb)
Roy Jiang (ctb)
Steven Kleinstein (aut, cph)

Citing

To cite the alakazam package in publications, please use:

Gupta N, Vander Heiden J, Uduman M, Gadala-Maria D, Yaari G and Kleinstein S (2015). “Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data.” Bioinformatics, pp. 1-3. doi: 10.1093/bioinformatics/btv359 (URL: http://doi.org/10.1093/bioinformatics/btv359).

To cite the Ig-specific lineage reconstruction and diversity methods, please use:

Stern J, Yaari G, Vander Heiden J, Church G, Donahue W, Hintzen R, Huttner A, Laman J, Nagra R, Nylander A, Pitt D, Ramanan S, Siddiqui B, Vigneault F, Kleinstein S, Hafler D and O’Connor K (2014). “B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes.” Science Translational Medicine, 6(248), pp. 248ra107. doi: 10.1126/scitranslmed.3008879 (URL: http://doi.org/10.1126/scitranslmed.3008879).