User-friendly R Wrapper to IgBLAST

---

Documentation for package ‘igblastr’ version 1.1.8

• 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()