igblastr

igblastr provides functions to install and use a local IgBLAST installation from within R for immunoglobulin and T-cell receptor sequence analysis.

Key Features:

• Local IgBLAST integration: Enables convenient installation and execution of a local IgBLAST installation directly from R.
• Preinstalled germline databases: Includes IgBLAST-compatible germline databases from OGRDB, the AIRR Community's Open Germline Receptor Database, for various organisms.
• Database installation from multiple sources: Provides functions to install additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or OGRDB, or from local FASTA files supplied by the user.
• Automated V and J allele annotation: Automatically generates and adds annotations for V and J alleles in new germline databases when possible, for use as replacements for the internal and auxiliary data provided by IgBLAST.

Scientific Applications:

• Adaptive immune receptor repertoire analysis: Facilitates analysis of immunoglobulin and T-cell receptor sequences by wrapping IgBLAST functionality in R.
• Germline database management: Supports construction and curation of custom IgBLAST-compatible germline databases from multiple reference sources.

Methodology:

Wraps a local IgBLAST installation for use within R; automatically generates V and J allele annotations for new germline databases to replace IgBLAST internal and auxiliary data.