# User-friendly R Wrapper to IgBLAST

## Documentation for package ‘igblastr’ version 1.0.8

- 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
auxdata-utils | Access or generate IgBLAST auxiliary data
auxdata_utils | Access or generate IgBLAST auxiliary data
bcr_browser | Display annotated BCR sequences in a browser
BLAST_USAGE_REPORT | Turn "Usage Reporting" on or off
compute_auxdata | Access or generate IgBLAST auxiliary data
download_paired_OAS_units | Download and manipulate OAS data
extract_codons | Extract and translate codons from a set of DNA sequences
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
fmt7-utils | igblastn output format 7
fmt7_utils | igblastn output format 7
get_auxdata_path | Access or generate IgBLAST auxiliary data
get_igblast_auxiliary_data | Access or generate 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
igdata_info | Update and manage IgBLAST auxiliary and internal data
IMGT_is_up | Install a germline db from IMGT
install_igblast | Install IgBLAST
install_IMGT_c_region_db | Install a germline db from IMGT
install_IMGT_germline_db | Install a germline db from IMGT
J_allele_has_stop_codon | Access or generate IgBLAST auxiliary data
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 | igblastn output format 7
list_paired_OAS_studies | Download and manipulate OAS data
list_paired_OAS_units | Download and manipulate OAS data
load_auxdata | Access or generate IgBLAST auxiliary 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 | Access or generate 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 | igblastn output format 7
outfmt7_utils | igblastn output format 7
parse_outfmt7 | igblastn output format 7
print.alignment_summary | igblastn output format 7
print.auxdata_md5sum_df | Update and manage IgBLAST auxiliary and internal data
print.c_region_dbs_df | List cached C-region dbs and select one to use with igblastn()
print.fmt7footer | igblastn output format 7
print.fmt7record | igblastn output format 7
print.germline_dbs_df | List cached germline dbs and select one to use with igblastn()
print.hit_table | igblastn output format 7
print.igblastn_raw_output | BLAST for BCR/Ig and TCR sequences
print.igblast_info | Check IgBLAST used by igblastr
print.igdata_info | Update and manage IgBLAST auxiliary and internal data
print.outfmt7_specifiers | igblastn output format 7
print.query_details | igblastn output format 7
print.subregion_sequence_details | igblastn output format 7
print.VDJ_junction_details | igblastn output format 7
print.VDJ_rearrangement_summary | igblastn output format 7
qseqid | igblastn output format 7
qseqid.fmt7record | igblastn output format 7
qseqid.query_details | igblastn output format 7
read_igblastn_AIRR_output | igblastn output format 19 (AIRR format)
read_igblastn_fmt7_output | igblastn output format 7
read_OAS_csv | Download and manipulate OAS data
read_OAS_csv_metadata | Download and manipulate OAS data
reset_live_igdata | Update and manage IgBLAST auxiliary and internal data
rm_c_region_db | List cached C-region dbs and select one to use with igblastn()
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 | 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
time_since_live_igdata_last_checked | Update and manage IgBLAST auxiliary and internal data
translate_codons | Extract and translate codons from a set of DNA sequences
translate_fwr4 | Access or generate IgBLAST auxiliary data
translate_J_alleles | Access or generate IgBLAST auxiliary data
update_live_igdata | Update and manage IgBLAST auxiliary and internal data
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()