blast_db.sql | Load SQL schema for blast_db |
BlastHeader-class | Class '"BlastHeader"' |
blastn | Wrapper for the NCBI Nucleotide-Nucleotide BLAST |
blastp | Wrapper for the NCBI Protein-Protein BLAST |
BlastParameters-class | Class '"BlastParameters"' |
blastr | A wrapper around NCBI Blast. |
blastReport | Parse NCBI BLAST XML files. |
BlastReport-class | Class '"BlastReport"' |
blastReportDB | Parse NCBI BLAST XML files into BlastReportDB objects. |
BlastReportDB-class | Class '"blastReportDB"' |
blastTable | Parse NCBI BLAST table files into BlastTable objects. |
BlastTable-class | Class '"BlastTable"' |
blastx | Wrapper for the NCBI Translated Query-Protein Subject BLAST |
coordinates | Access components of High-Scoring Pairs (HSPs) |
db_bulk_insert | Insert a 'data.frame' into a corresponding SQLite table |
db_connect | Connect to an existing SQLite database. |
db_count | Count rows in a db table |
db_create | Create an SQLite database. |
db_disconnect | Disconnect from an SQLite database. |
db_info | Metadata for an SQLite database. |
db_is_current | Is a connection to an SQLite database still current. |
db_list_fields | List available tables in an SQLite database |
db_list_tables | List available tables in an SQLite database |
db_query | Query an SQLite database. |
Defline-class | Class '"Defline"' |
Deflines | Parse fasta definition lines |
DeflineSet-class | Class '"DeflineSet"' of '"Defline"' objects |
do_log | Log a message to stderr. |
dot_blast | Wrapper for the new NCBI BLAST+ tools |
getAccession | Access components of BLAST Hits |
getAlignLen | Access components of High-Scoring Pairs (HSPs) |
getDefline | Access components of BLAST Hits |
getGaps | Access components of High-Scoring Pairs (HSPs) |
getGeneID | Access components of BLAST Hits |
getHeader | Extract the header of a BLAST report |
getHit | Access components of BLAST Queries |
getHitCoverage | Extract the total Hit Coverage. |
getHitDef | Access components of BLAST Hits |
getHitID | Access components of BLAST Hits |
getHitLen | Access components of BLAST Hits |
getHitNum | Access components of BLAST Hits |
getHsp | Access components of BLAST Hits |
getHspHitID | Access components of BLAST Hits |
getHspID | Access components of BLAST Hits |
getHspNum | Access components of High-Scoring Pairs (HSPs) |
getIdentity | Access components of High-Scoring Pairs (HSPs) |
getParams | Extract parameters and statistics from a BLAST report |
getPercGaps | Access components of High-Scoring Pairs (HSPs) |
getPercIdentity | Access components of High-Scoring Pairs (HSPs) |
getPercPositive | Access components of High-Scoring Pairs (HSPs) |
getPositive | Access components of High-Scoring Pairs (HSPs) |
getQuery | Extract queries from a BLAST report |
getQueryCoverage | Extract the total Query Coverage. |
getQueryDef | Access components of BLAST Queries |
getQueryID | Access components of BLAST Queries |
getQueryLen | Access components of BLAST Queries |
getQueryNum | Access components of BLAST Queries |
has_command | Test if an external executable is available |
has_tables | Check if a SQLite database has specified tables |
Hit-class | Class '"Hit"' |
HitList-class | Class '"HitList"' of '"Hit"' objects |
Hsp-class | Class '"Hsp"' |
HspList-class | Class '"HspList"' of '"Hsp"' objects |
linebreak | Format paragraphs |
makeblasttdb | Wrapper for NCBI makeblastdb |
make_deflines | Construct deflines |
nhits | Access components of BLAST Queries |
nhsps | Access components of BLAST Hits |
qblast | Do a BLAST search using the QBLAST URL API |
Query-class | Class '"Query"' |
QueryList-class | Class '"QueryList"' of '"Query"' objects |
rpsblast | Wrapper for the NCBI Reversed Position Specific Blast |
scores | Access components of High-Scoring Pairs (HSPs) |
sequence | Access components of High-Scoring Pairs (HSPs) |
SQLiteDB-class | Class '"SQLiteDB"' |
SysCall | Wrapper for system commands |
tblastn | Wrapper for the NCBI Protein Query-Translated Subject BLAST |
tblastx | Wrapper for the NCBI Translated Query-Protein Subject BLAST |
timestamp | Generate a timestamp string. |
update_blastdb | Wrapper for 'update_blastdb' |
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