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:
- 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.
- Providing an R interface for interacting with the output of the pRESTO and Change-O tool suites.
- Performing clonal abundance and diversity analysis on lymphocyte
repertoires.
- Performing lineage reconstruction on clonal populations of Ig
sequences and analyzing the topology of the resultant lineage
trees.
- Performing physicochemical property analyses of lymphocyte receptor
sequences.
For help and questions, please contact the
Immcantation Group
or use the issue
tracker.