alakazam {alakazam}R Documentation

The alakazam package

Description

alakazam in a member of the Immcantation framework of tools and serves five main purposes:

For additional details regarding the use of the alakazam package see the vignettes:
browseVignettes("alakazam")

File I/O

Sequence cleaning

Lineage reconstruction

Lineage topology analysis

Diversity analysis

Ig and TCR sequence annotation

Sequence distance calculation

Amino acid propertes

References

  1. Vander Heiden JA, Yaari G, et al. pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires. Bioinformatics. 2014 30(13):1930-2.

  2. Stern JNH, Yaari G, Vander Heiden JA, et al. B cells populating the multiple sclerosis brain mature in the draining cervical lymph nodes. Sci Transl Med. 2014 6(248):248ra107.

  3. Wu Y-CB, et al. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. J Allergy Clin Immunol. 2014 134(3):604-12.

  4. Gupta NT, Vander Heiden JA, et al. Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data. Bioinformatics. 2015 Oct 15;31(20):3356-8.


[Package alakazam version 1.1.0 Index]