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

check_csvCheck the metadata csv files and write only the 'good'...
check_filesList the directory containing the various sqlite files and...
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.
download_uniprot_annotationsMake a table of uniprot anntotations when possible.
download_uniprot_proteomeDownload the txt uniprot data for a given accession/species
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_eupath_metadata() using all the sub-projects...
get_eupath_entrySearch the eupathdb metadata for a given species substring.
get_eupath_fieldsExtract query-able fields from the EupathDb.
get_eupath_pkgnamesGenerate standardized package names for the various eupathdb...
get_kegg_orgnSearch KEGG identifiers for a given species name.
get_orthologs_all_genesQuery ortholog tables from the eupathdb one gene at a time.
get_orthologs_one_geneThis peculiar and slow querying of orthologs is due to me...
grapes-colon-colon-colon-grapesR CMD check is super annoying about :::.
kegg_vector_to_dfConvert a potentially non-unique vector from kegg into a...
load_eupath_annotationsShortcut for loading annotation data from a eupathdb-based...
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.
load_uniprot_annotationsRead a uniprot text file and extract as much information from...
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_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_annotationsGather all available annotation data for a given 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_pubmed_tableUse the post interface to get linkout data.
post_eupath_rawThe new eupath system provides 3 output types for downloading...
post_eupath_snp_tableUse the post interface to get SNP data.
post_eupath_tableQueries one of the EuPathDB APIs using a POST request and...
start_eupathdbGet started with EuPathDB
write_eupath_metadataStandardize the writing of csv metadata.
xref_speciesCross reference the taxonomy data from...
xref_taxonomyCross reference the taxonomy data from GenomeInfoDb with...
khughitt/EuPathDB documentation built on Sept. 10, 2019, 8:26 p.m.