User-friendly R Wrapper to IgBLAST

Documentation for package ‘igblastr’ version 1.1.28

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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-utils	Access IgBLAST auxiliary data
auxdata_IO	Read/write IgBLAST auxiliary data files
auxdata_utils	Access IgBLAST auxiliary data

-- B --

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

-- C --

compute_auxdata	Compute IgBLAST auxiliary data
compute_germline_db_auxdata	Access IgBLAST auxiliary data
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_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 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_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
intdata	Access IgBLAST internal data
intdata-utils	Access IgBLAST internal data
intdata_utils	Access IgBLAST internal data

-- 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
load_auxdata	Access 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 IgBLAST auxiliary data
load_intdata	Access IgBLAST internal data

-- M --

makeblastdb_version

Check IgBLAST used by igblastr

-- N --

ndm_data-IO	Read/write "ndm" files
ndm_data_IO	Read/write "ndm" files

-- 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
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_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_ndm_data	Read/write "ndm" files
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	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_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	Access IgBLAST internal data

-- W --

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