User-friendly R Wrapper to IgBLAST


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Documentation for package ‘igblastr’ version 0.99.11

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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 the 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 Ig and TCR sequences
igblastn_help BLAST for 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
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 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
summary.query_details Handle igblastn output format 7
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()