Man pages for gschofl/ncbi
Retrieve data from NCBI.
| clear_cache | Clear the contents of the lineage cache |
| Collection-class | Collection-class |
| collectionConstructor | Create a constructor function for a Collection class. |
| collectionShower | Create a show-method for a Collection class. |
| collectionValidator | Create a validity-checking method for a Collection class. |
| Connection-classes | Database Connections |
| 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_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. |
| doi-class | doi-class |
| EST | Retrieve sequences and annotations from the EST database |
| fetch_files | Fetch files from a remote location conditional on a... |
| file_compare | Compare local and remote file timestamp and/or size |
| getByRank | Extract taxa from a lineage by their rank |
| GSS | Retrieve sequences and annotations from the GSS database |
| has_command | Test if an external executable is available |
| has_tables | Check if a SQLite database has specified tables |
| Lineage | Construct a Lineage |
| linebreak | Format paragraphs |
| makeCollectionClass | Create a Collection Class Definition |
| ncbi | Retrieve and parse data from NCBI databases. |
| new_cache | Register a caching environment |
| new_taxon | Extract taxon from taxon.db |
| nucleotide | Retrieve sequences and annotations from the Nucleotide... |
| parseGenBank | Parse GenBank flatfiles |
| parseTSeqSet | Parse Tiny Bioseq FASTA files |
| protein | Retrieve sequences and annotations from the Protein database |
| pubmed | Retrieve records from the PubMed database. |
| pubmed-class | pubmed-class |
| pubmed-methods | Access pubmed objects |
| rBind | Bind a list of data frames |
| show_cache | Show contents of the lineage cache |
| sqliteDB-class | sqliteDB-class |
| strip_ext | Strip file extensions |
| Taxon-accessors | Taxon accessors |
| Taxon-class | Taxon-classes |
| taxon-constructors | Retrieve records from the NCBI Taxonomy database (locally or... |
| TaxonDB | Create a local install of the NCBI Taxonomy database. |
| taxonDBConnect | Create connections to a local NCBI Taxonomy or GeneID... |
| TaxonList | TaxonList and LineageList |
