# User-friendly R Wrapper to IgBLAST

## Documentation for package ‘igblastr’ version 1.2.19

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G H I J L M N O P Q R S T U V W

## -- A --

allele2gene | Go from germline gene allele names to germline gene names
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 | Access IgBLAST auxiliary data
auxdata-IO | Read/write IgBLAST auxiliary data files
auxdata-misc | Miscellaneous auxiliary data utilities
auxdata_IO | Read/write IgBLAST auxiliary data files
auxdata_misc | Miscellaneous auxiliary data utilities

## -- B --

bcr_browser | Display annotated BCR sequences in a browser
BLAST_USAGE_REPORT | Turn "Usage Reporting" on or off

## -- C --

combine_c_region_dbs | Combine two existing germline dbs
combine_germline_dbs | Combine two existing germline dbs
compute_auxdata | Compute IgBLAST auxiliary data
compute_germline_db_auxdata | Miscellaneous auxiliary data utilities
compute_imgt_intdata | Compute V gene delineations
compute_V_gene_delineations | Compute V gene delineations

## -- D --

download_IMGT_germline_sequences | Download germline sequences from IMGT
download_OGRDB_germline_json | Download AIRR-C JSON files from OGRDB
download_OGRDB_germline_sequences | Download germline sequences from OGRDB
download_paired_OAS_units | Download and manipulate OAS data

## -- E --

extract_auxdata_from_ogrdb_json | Download AIRR-C JSON files from OGRDB
extract_codons | Extract and translate codons from a set of DNA sequences
extract_intdata_from_ogrdb_json | Download AIRR-C JSON files from OGRDB
extract_metadata_from_OAS_units | Download and manipulate OAS data
extract_region_length | Extract region of interest from a set of analyzed sequences
extract_region_net_charge | Compute the net charges of amino acid sequences
extract_sequences_from_paired_OAS_df | Download and manipulate OAS data
extract_sequences_from_paired_OAS_units | Download and manipulate OAS data
extract_sequence_region | Extract region of interest from a set of analyzed sequences

## -- F --

fmt7-utils | igblastn output format 7
fmt7_utils | igblastn output format 7

## -- G --

get_auxdata_path | Access IgBLAST auxiliary data
get_igblast_auxiliary_data | Access IgBLAST auxiliary data
get_igblast_root | Control IgBLAST installation to use
get_intdata_path | Access IgBLAST internal data

## -- H --

has_igblast | Check IgBLAST used by igblastr

## -- I --

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_FWRCDR_ENDS | Compute V gene delineations
IMGT_is_up | Download germline sequences from IMGT
install_custom_germline_db | Install a germline db from user-supplied gene allele sequences
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
install_OGRDB_germline_db | Install a germline db from OGRDB germline sets
intdata | Access IgBLAST internal data
intdata-misc | Miscellaneous internal data utilities
intdata_misc | Miscellaneous internal data utilities

## -- J --

J_alleles-inspect | Basic inspection of J allele sequences
J_alleles_inspect | Basic inspection of J allele sequences
J_allele_has_stop_codon | Basic inspection of J allele sequences

## -- L --

list_c_region_dbs | List cached C-region dbs
list_germline_dbs | List cached germline dbs
list_igblast_organisms | Check IgBLAST used by igblastr
list_IMGT_organisms | Download germline sequences from IMGT
list_IMGT_releases | Download germline sequences 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
live_igdata | Update and manage IgBLAST auxiliary and internal data
load_auxdata | Access IgBLAST auxiliary data
load_c_region_db | Select cached C-region db to use with igblastn()
load_c_region_sequences | Select cached C-region db to use with igblastn()
load_germline_db | Select cached germline db to use with igblastn()
load_germline_sequences | Select cached germline db to use with igblastn()
load_igblast_auxiliary_data | Access IgBLAST auxiliary data
load_intdata | Access IgBLAST internal data

## -- M --

makeblastdb_version | Check IgBLAST used by igblastr
make_auxdata_files_from_ogrdb_jsons | Install a germline db from OGRDB germline sets
make_intdata_files_from_ogrdb_jsons | Install a germline db from OGRDB germline sets

## -- N --

ndm_data-IO | Read/write "ndm" files
ndm_data_IO | Read/write "ndm" files
net_charge | Compute the net charges of amino acid sequences

## -- O --

OAS-utils | Download and manipulate OAS data
OAS_is_up | Download and manipulate OAS data
OAS_utils | Download and manipulate OAS data
outfmt7-utils | igblastn output format 7
outfmt7_utils | igblastn output format 7

## -- P --

parse_imgt_fasta_headers | Parse IMGT FASTA headers
parse_outfmt7 | igblastn output format 7
percent_mutation | Computes percent mutation in V, D, J segments
PKA_VALUES | Compute the net charges of amino acid sequences
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
print.fmt7footer | igblastn output format 7
print.fmt7record | igblastn output format 7
print.germline_dbs_df | List cached germline dbs
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
print_J_alleles | Basic inspection of J allele sequences

## -- Q --

qseqid | igblastn output format 7
qseqid.fmt7record | igblastn output format 7
qseqid.query_details | igblastn output format 7

## -- R --

read_auxdata | Read/write IgBLAST auxiliary data files
read_igblastn_AIRR_output | igblastn output format 19 (AIRR format)
read_igblastn_fmt7_output | igblastn output format 7
read_ndm_data | Read/write "ndm" files
read_OAS_csv | Download and manipulate OAS data
read_OAS_csv_metadata | Download and manipulate OAS data
remove_gaps | Extract and translate codons from a set of DNA sequences
reset_c_region_dbs | Reset the cached C-region dbs
reset_germline_dbs | Reset the cached germline dbs
reset_live_igdata | Update and manage IgBLAST auxiliary and internal data
rm_c_region_db | List cached C-region dbs
rm_germline_db | List cached germline dbs

## -- S --

same_alleles_annot | Read/write "ndm" files
set_igblast_root | Control IgBLAST installation to use
show_intdata_disagreements | Miscellaneous internal data utilities
solve_cdr3_ends_using_fwr4_aa_comparisons | Compute IgBLAST auxiliary data
solve_cdr3_ends_using_fwr4_dna_comparisons | Compute IgBLAST auxiliary data
solve_cdr3_ends_using_fwr4_dna_PWM | Compute IgBLAST auxiliary data
summarizeMismatches | Summarize mismatches and indels between query and germline sequences
summary.query_details | igblastn output format 7

## -- T --

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 | Basic inspection of J allele sequences
translate_J_alleles | Basic inspection of J allele sequences
translate_V_alleles | Basic inspection of V allele sequences

## -- U --

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 | Select cached C-region db to use with igblastn()
use_germline_db | Select cached germline db to use with igblastn()

## -- V --

validate_and_complete_auxdata_with_ref | Compute IgBLAST auxiliary data
validate_ndm_rows | Read/write "ndm" files
V_alleles-inspect | Basic inspection of V allele sequences
V_alleles_inspect | Basic inspection of V allele sequences
V_allele_has_stop_codon | Basic inspection of V allele sequences
V_genes_with_varying_fwrcdr_boundaries | Miscellaneous internal data utilities

## -- W --

write_auxdata | Read/write IgBLAST auxiliary data files
write_ndm_data | Read/write "ndm" files