User-friendly R Wrapper to IgBLAST

Documentation for package ‘igblastr’ version 1.1.13

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

-- A --

allele2gene	Go from germline gene allele names to germline gene names
annotate_heavy_V_alleles	Access and manipulate IgBLAST internal data
annotate_light_V_alleles	Access and manipulate IgBLAST internal data
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, manipulate, and generate IgBLAST auxiliary data
auxdata-utils	Access, manipulate, and generate IgBLAST auxiliary data
auxdata_utils	Access, manipulate, and generate IgBLAST auxiliary data

-- B --

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

-- C --

check_V_ndm_data	Extract V gene FWR/CDR annotation from OGRDB JSON file
compute_auxdata	Compute IgBLAST auxiliary data
compute_imgt_intdata	Compute IgBLAST internal data

-- D --

download_paired_OAS_units

Download and manipulate OAS data

-- E --

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

-- F --

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

-- G --

get_auxdata_path	Access, manipulate, and generate IgBLAST auxiliary data
get_igblast_auxiliary_data	Access, manipulate, and generate IgBLAST auxiliary data
get_igblast_root	Control IgBLAST installation to use
get_intdata_path	Access and manipulate 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_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
intdata	Access and manipulate IgBLAST internal data
intdata-utils	Access and manipulate IgBLAST internal data
intdata_utils	Access and manipulate IgBLAST internal data

-- J --

J_allele_has_stop_codon

Access, manipulate, and generate IgBLAST auxiliary data

-- 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	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, manipulate, and generate IgBLAST auxiliary data
load_c_region_db	Select cached C-region db to use with igblastn()
load_germline_db	Select cached germline db to use with igblastn()
load_igblast_auxiliary_data	Access, manipulate, and generate IgBLAST auxiliary data
load_intdata	Access and manipulate IgBLAST internal data

-- M --

makeblastdb_version	Check IgBLAST used by igblastr
makeogrannote	Extract V gene FWR/CDR annotation from OGRDB JSON file

-- O --

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

-- P --

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
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

-- Q --

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

-- R --

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
read_V_ndm_data	Extract V gene FWR/CDR annotation from OGRDB JSON file
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 --

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

-- 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	Access, manipulate, and generate IgBLAST auxiliary data
translate_J_alleles	Access, manipulate, and generate IgBLAST auxiliary data
translate_V_alleles	Access and manipulate IgBLAST internal data

-- 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 --

V_allele_has_stop_codon	Access and manipulate IgBLAST internal data
V_genes_with_varying_fwrcdr_boundaries	Access and manipulate IgBLAST internal data

-- W --

write_V_ndm_data

Extract V gene FWR/CDR annotation from OGRDB JSON file