Man pages for khughitt/EuPathDB
Provides access to pathogen annotation resources available on EuPathDB databases

buildBoolean to see if packages should be built by devtools.
build_dirSet the build directory
check_csvCheck the metadata csv files and write only the 'good'...
check_filesList the directory containing the various sqlite files and...
check_post_resultcheck that the result from a post makes sense.
check_rdaCheck the status of a saved database. I save a bunch of rda...
check_s3Check the metadata csv files and write only the 'good'...
choose_successful_postChoose a successful organism string when sending a POST
clean_pkgCleans up illegal characters in packages generated by...
copy_s3_fileCopy the relevant file for each data type into a place which...
download_eupath_metadataReturns metadata for all eupathdb organisms.
errorError-level logging function.
EuPathDBEuPathDB: Access EuPathDB annotations using AnnotationHub
extract_eupath_orthologsGiven 2 species names from the eupathdb, make orthology...
extract_gene_locationsClean up the gene location field from eupathdb derived gene...
get_all_metadataInvoke download_eupathdb_metadata() using all the...
get_eupath_entrySearch the eupathdb metadata for a given species substring.
get_eupath_pkgnamesGenerate standardized package names for the various eupathdb...
get_kegg_orgnSearch KEGG identifiers for a given species name.
get_metadata_filenameCreate a list of output csv filenames containing the metadata...
get_rda_filenameProvide the filename for a temporary rda file for saving data...
get_semantic_columnsHaha this is nasty, extract interesting data columns from the...
get_versionsDownload the current eupathdb version.
grapes-colon-colon-colon-grapesR CMD check is super annoying about :::.
infoInfo-level logging function.
kegg_vector_to_dfConvert a potentially non-unique vector from kegg into a...
load_ah_annotationsShortcut for loading annotation data from AnnotationHub,...
load_eupath_annotationsShortcut for loading annotation data from a eupathdb-based...
load_eupath_goShortcut for loading annotation data from a eupathdb-based...
load_eupath_pkgLoads a pkg into the current R environment.
load_kegg_annotationsCreate a data frame of pathways to gene IDs from KEGGREST
load_orgdb_annotationsLoad organism annotation data from an orgdb sqlite package.
load_orgdb_goRetrieve GO terms associated with a set of genes.
make_eupath_bsgenomeGenerate a BSgenome package from the eupathdb.
make_eupath_grangesGenerate a GRanges rda savefile from a gff file.
make_eupath_organismdbiCreate an organismDbi instance for an eupathdb organism.
make_eupath_orgdbCreate an orgdb SQLite database from the tables in eupathdb.
make_eupath_txdbGenerate an EuPathDB organism TxDb package.
make_get_queryCreate a GET query to try out. Here is the string...
make_post_attemptsCreate POST queries to try out.
make_taxon_namesIterate through the various ways of representing taxon names
move_final_packageMove a package file to its final location for collation by...
orgdb_from_ahGet an orgdb from an AnnotationHub taxonID.
pipePipe operator
post_eupath_annotationsCreate a series of POST requests which download all the...
post_eupath_goslim_tableUse the POST interface to get GO data from the EuPathDB.
post_eupath_go_tableUse the POST interface to get GO data from the EuPathDB.
post_eupath_interpro_tableUse the post interface to get interpro data.
post_eupath_linkout_tableUse the post interface to get linkout data.
post_eupath_ortholog_tableUse the post interface to get ortholog data.
post_eupath_pathway_tableUse the post interface to get pathway data.
post_eupath_pdb_tableUse the post interface to get linkout data.
post_eupath_pubmed_tableUse the post interface to get linkout data.
post_eupath_tableQueries one of the EuPathDB APIs using a POST request.
prefix_mapA few webservices at the eupathdb are not what one would...
print.downloaded_metadataPrint a representation of some downloaded metadata.
query_s3_ahAs yet another test, this function will download all the AH...
query_s3_filePerform what should be a completely silly final check on the...
query_s3_grangesPerform what should be a completely silly final check on the...
query_s3_orgdbPerform what should be a completely silly final check on the...
query_s3_txdbPerform what should be a completely silly final check on the...
remove_eupath_nasGet rid of spurious NA entries in a table from the eupathdb.
search_na_taxonTry harder to fill in the taxonomy ID number.
smSilence
warnWarning-level logging function.
write_eupath_metadataStandardize the writing of csv metadata.
xref_ah_speciesCross reference the taxonomy data from...
xref_gidb_speciesCross reference information from the taxonDB vs. the...
xref_taxonomy_numberCross reference the taxonomy data from GenomeInfoDb with...
khughitt/EuPathDB documentation built on Nov. 4, 2023, 4:19 a.m.