Package: igblastr 1.3.15

Introduction | Install and load the package | Install and check IgBLAST | Install IgBLAST | Check IgBLAST | Install and select an IgBLAST-compatible germline database | Built-in germline databases | Install additional IgBLAST-compatible germline databases | Install an IgBLAST-compatible germline database from IMGT/V-QUEST | Install an IgBLAST-compatible germline database from user-supplied gene allele sequences | Select the germline database to use with igblastn() | Internal data and auxiliary data | What are the internal data and auxiliary data? | IgBLAST-provided internal/auxiliary data | igblastr-generated internal/auxiliary data | How is this data generated? | How to use the igblastr-generated internal/auxiliary data with igblastr? | Select a constant region database (optional) | Use igblastn() | Prepare the query sequences | Call igblastn() on the query sequences | Downstream analysis | Distribution of percent mutation across BCR sequences | Distribution of germline genes | Lengths and motifs of CDR3 sequences | Advanced usage | Passing additional arguments to igblastn() | Restrict the search to a subset of user-supplied gene alleles | Combine germline databases from two different organisms | Create the hybrid germline database | A quick look at columns v_call, d_call, and j_call | A TCR analysis example | Prepare the TCR query sequences | Install a TCR germline database | Select a TCR constant region database (optional) | Call igblastn() on the TCR query sequences | Future developments and session information | Future developments | Session information