Man pages for khughitt/EuPathDB
Provides access to pathogen annotation resources available on EuPathDB databases
| build | Boolean to see if packages should be built by devtools. |
| build_dir | Set the build directory |
| check_csv | Check the metadata csv files and write only the 'good'... |
| check_files | List the directory containing the various sqlite files and... |
| check_post_result | check that the result from a post makes sense. |
| check_rda | Check the status of a saved database. I save a bunch of rda... |
| check_s3 | Check the metadata csv files and write only the 'good'... |
| choose_successful_post | Choose a successful organism string when sending a POST |
| clean_pkg | Cleans up illegal characters in packages generated by... |
| copy_s3_file | Copy the relevant file for each data type into a place which... |
| download_eupath_metadata | Returns metadata for all eupathdb organisms. |
| error | Error-level logging function. |
| EuPathDB | EuPathDB: Access EuPathDB annotations using AnnotationHub |
| extract_eupath_orthologs | Given 2 species names from the eupathdb, make orthology... |
| extract_gene_locations | Clean up the gene location field from eupathdb derived gene... |
| get_all_metadata | Invoke download_eupathdb_metadata() using all the... |
| get_eupath_entry | Search the eupathdb metadata for a given species substring. |
| get_eupath_pkgnames | Generate standardized package names for the various eupathdb... |
| get_kegg_orgn | Search KEGG identifiers for a given species name. |
| get_metadata_filename | Create a list of output csv filenames containing the metadata... |
| get_rda_filename | Provide the filename for a temporary rda file for saving data... |
| get_semantic_columns | Haha this is nasty, extract interesting data columns from the... |
| get_versions | Download the current eupathdb version. |
| grapes-colon-colon-colon-grapes | R CMD check is super annoying about :::. |
| info | Info-level logging function. |
| kegg_vector_to_df | Convert a potentially non-unique vector from kegg into a... |
| load_ah_annotations | Shortcut for loading annotation data from AnnotationHub,... |
| load_eupath_annotations | Shortcut for loading annotation data from a eupathdb-based... |
| load_eupath_go | Shortcut for loading annotation data from a eupathdb-based... |
| load_eupath_pkg | Loads a pkg into the current R environment. |
| load_kegg_annotations | Create a data frame of pathways to gene IDs from KEGGREST |
| load_orgdb_annotations | Load organism annotation data from an orgdb sqlite package. |
| load_orgdb_go | Retrieve GO terms associated with a set of genes. |
| make_eupath_bsgenome | Generate a BSgenome package from the eupathdb. |
| make_eupath_granges | Generate a GRanges rda savefile from a gff file. |
| make_eupath_organismdbi | Create an organismDbi instance for an eupathdb organism. |
| make_eupath_orgdb | Create an orgdb SQLite database from the tables in eupathdb. |
| make_eupath_txdb | Generate an EuPathDB organism TxDb package. |
| make_get_query | Create a GET query to try out. Here is the string... |
| make_post_attempts | Create POST queries to try out. |
| make_taxon_names | Iterate through the various ways of representing taxon names |
| move_final_package | Move a package file to its final location for collation by... |
| orgdb_from_ah | Get an orgdb from an AnnotationHub taxonID. |
| pipe | Pipe operator |
| post_eupath_annotations | Create a series of POST requests which download all the... |
| post_eupath_goslim_table | Use the POST interface to get GO data from the EuPathDB. |
| post_eupath_go_table | Use the POST interface to get GO data from the EuPathDB. |
| post_eupath_interpro_table | Use the post interface to get interpro data. |
| post_eupath_linkout_table | Use the post interface to get linkout data. |
| post_eupath_ortholog_table | Use the post interface to get ortholog data. |
| post_eupath_pathway_table | Use the post interface to get pathway data. |
| post_eupath_pdb_table | Use the post interface to get linkout data. |
| post_eupath_pubmed_table | Use the post interface to get linkout data. |
| post_eupath_table | Queries one of the EuPathDB APIs using a POST request. |
| prefix_map | A few webservices at the eupathdb are not what one would... |
| print.downloaded_metadata | Print a representation of some downloaded metadata. |
| query_s3_ah | As yet another test, this function will download all the AH... |
| query_s3_file | Perform what should be a completely silly final check on the... |
| query_s3_granges | Perform what should be a completely silly final check on the... |
| query_s3_orgdb | Perform what should be a completely silly final check on the... |
| query_s3_txdb | Perform what should be a completely silly final check on the... |
| remove_eupath_nas | Get rid of spurious NA entries in a table from the eupathdb. |
| search_na_taxon | Try harder to fill in the taxonomy ID number. |
| sm | Silence |
| warn | Warning-level logging function. |
| write_eupath_metadata | Standardize the writing of csv metadata. |
| xref_ah_species | Cross reference the taxonomy data from... |
| xref_gidb_species | Cross reference information from the taxonDB vs. the... |
| xref_taxonomy_number | Cross reference the taxonomy data from GenomeInfoDb with... |
