# User-friendly R Wrapper to IgBLAST

## Documentation for package ‘igblastr’ version 1.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

augment_germline_db | Add novel gene alleles to a germline db
augment_germline_db_D | Add novel gene alleles to a germline db
augment_germline_db_J | Add novel gene alleles to a germline db
augment_germline_db_V | Add novel gene alleles to a germline db
auxiliary-data-utils | Manipulation of IgBLAST auxiliary data
auxiliary_data_utils | Manipulation of IgBLAST auxiliary data
bcr_browser | Display annotated BCR sequences in a browser
BLAST_USAGE_REPORT | Turn "Usage Reporting" on or off
download_paired_OAS_units | Download and manipulate OAS data
extract_metadata_from_OAS_units | Download and manipulate OAS data
extract_sequences_from_paired_OAS_df | Download and manipulate OAS data
extract_sequences_from_paired_OAS_units | Download and manipulate OAS data
get_igblast_auxiliary_data | Manipulation of IgBLAST auxiliary data
get_igblast_root | Control IgBLAST installation to use
has_igblast | Check IgBLAST used by igblastr
igblastn | BLAST for BCR/Ig and TCR sequences
igblastn_help | BLAST for BCR/Ig and TCR sequences
igblastn_version | Check IgBLAST used by igblastr
igblastr_usage_report | Turn "Usage Reporting" on or off
igblast_build | Check IgBLAST used by igblastr
igblast_info | Check IgBLAST used by igblastr
IGBLAST_ROOT | Use an external IgBLAST installation
igbrowser | Display annotated BCR sequences in a browser
IMGT_is_up | Install a germline db from IMGT
install_igblast | Install IgBLAST
install_IMGT_germline_db | Install a germline db from IMGT
list_c_region_dbs | List cached C-region dbs and select one to use with igblastn()
list_germline_dbs | List cached germline dbs and select one to use with igblastn()
list_igblast_organisms | Check IgBLAST used by igblastr
list_IMGT_organisms | Install a germline db from IMGT
list_IMGT_releases | Install a germline db from IMGT
list_outfmt7_specifiers | Handle igblastn output format 7
list_paired_OAS_studies | Download and manipulate OAS data
list_paired_OAS_units | Download and manipulate OAS data
load_c_region_db | List cached C-region dbs and select one to use with igblastn()
load_germline_db | List cached germline dbs and select one to use with igblastn()
load_igblast_auxiliary_data | Manipulation of IgBLAST auxiliary data
makeblastdb_version | Check IgBLAST used by igblastr
OAS-utils | Download and manipulate OAS data
OAS_utils | Download and manipulate OAS data
outfmt7-utils | Handle igblastn output format 7
parse_outfmt7 | Handle igblastn output format 7
print.alignment_summary | Handle igblastn output format 7
print.c_region_dbs_df | List cached C-region dbs and select one to use with igblastn()
print.fmt7footer | Handle igblastn output format 7
print.fmt7record | Handle igblastn output format 7
print.germline_dbs_df | List cached germline dbs and select one to use with igblastn()
print.hit_table | Handle igblastn output format 7
print.igblastn_raw_output | BLAST for BCR/Ig and TCR sequences
print.igblast_info | Check IgBLAST used by igblastr
print.outfmt7_specifiers | Handle igblastn output format 7
print.query_details | Handle igblastn output format 7
print.subregion_sequence_details | Handle igblastn output format 7
print.VDJ_junction_details | Handle igblastn output format 7
print.VDJ_rearrangement_summary | Handle igblastn output format 7
qseqid | Handle igblastn output format 7
qseqid.fmt7record | Handle igblastn output format 7
qseqid.query_details | Handle igblastn output format 7
read_OAS_csv | Download and manipulate OAS data
read_OAS_csv_metadata | Download and manipulate OAS data
rm_germline_db | List cached germline dbs and select one to use with igblastn()
set_igblast_root | Control IgBLAST installation to use
summarizeMismatches | Summarize mismatches and indels between query and germline sequences
summary.query_details | Handle igblastn output format 7
tabulate_deletions | Summarize mismatches and indels between query and germline sequences
tabulate_insertions | Summarize mismatches and indels between query and germline sequences
tabulate_mismatches | Summarize mismatches and indels between query and germline sequences
Usage_report | Turn "Usage Reporting" on or off
usage_report | Turn "Usage Reporting" on or off
Usage_reporting | Turn "Usage Reporting" on or off
usage_reporting | Turn "Usage Reporting" on or off
use_c_region_db | List cached C-region dbs and select one to use with igblastn()
use_germline_db | List cached germline dbs and select one to use with igblastn()