igblastr

User-friendly R Wrapper to IgBLAST

Bioconductor version: 3.23 · Package version: 1.2.17

The igblastr package provides functions to conveniently install and use a local IgBLAST installation from within R. The package also includes a set of built-in IgBLAST-compatible germline databases from OGRDB, the AIRR Community’s Open Germline Receptor Database, for various organisms. It provides functions to create additional IgBLAST-compatible germline databases using reference sequences retrieved from IMGT/V-QUEST or local FASTA files supplied by the user. When possible, annotations for the V and J alleles in a new germline database are automatically generated and added to the database, so they can be used as replacements for the internal and auxiliary data provided by IgBLAST. IgBLAST is described at <https://pubmed.ncbi.nlm.nih.gov/23671333/>. IgBLAST web interface: <https://www.ncbi.nlm.nih.gov/igblast/>. OGRDB: <https://ogrdb.airr-community.org/>. IMGT/V-QUEST download site: <https://www.imgt.org/download/V-QUEST/>.

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("igblastr")