User-friendly R Wrapper to IgBLAST

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Documentation for package ‘igblastr’ version 0.99.18

• 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
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()