Description
Immunoglobulin Clonal Lineage and Diversity Analysis.
Description
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>.
README.md
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.
Contact
For help and questions, please contact the Immcantation Group or use the issue tracker.