Files in khughitt/EuPathDB

Provides access to pathogen annotation resources available on EuPathDB databases

R/check_csv.R R/check_files.R R/check_rda.R R/check_s3.R R/clean_pkg.R R/copy_s3_file.R R/download_eupath_metadata.R R/eupathdb.R R/expand_list_columns.R R/extract_eupath_orthologs.R R/extract_gene_locations.R R/get_all_metadata.R R/get_eupath_annotation_columns.R R/get_eupath_entry.R R/get_eupath_gene_types.R R/get_eupath_pkgnames.R R/get_kegg_orgn.R R/get_metadata_filename.R R/get_semantic_columns.R R/get_tags.R R/get_versions.R R/kegg_vector_to_df.R R/load_ah_annotations.R R/load_eupath_annotations.R R/load_eupath_go.R R/load_eupath_pkg.R R/load_kegg_annotations.R R/load_orgdb_annotations.R R/load_orgdb_go.R R/logging.R R/make_eupath_bsgenome.R R/make_eupath_granges.R R/make_eupath_organismdbi.R R/make_eupath_orgdb.R R/make_eupath_txdb.R R/make_taxon_names.R R/move_final_package.R R/orgdb_from_ah.R R/post_eupath_annotations.R R/post_eupath_go.R R/post_eupath_goslim.R R/post_eupath_interpro.R R/post_eupath_linkout.R R/post_eupath_ortholog.R R/post_eupath_pathway.R R/post_eupath_pdb.R R/post_eupath_pubmed.R R/post_eupath_table.R R/prefix_map.R R/query_s3_ah.R R/query_s3_file.R R/remove_eupath_nas.R R/test_helpers.R R/write_eupath_metadata.R R/xref_species.R R/xref_taxonomy.R R/zzz_print.R README.md inst/doc/EuPathDB.R inst/doc/EuPathDB_AnnotationHub_Tutorial.R inst/doc/EuPathDB_AnnotationHub_Tutorial.Rmd inst/doc/EuPathDB_Developers_Guide.R inst/doc/EuPathDB_Developers_Guide.Rmd inst/doc/EuPathDB_Package_Generation_Tutorial.R inst/doc/EuPathDB_Package_Generation_Tutorial.Rmd inst/doc/EuPathDB_trey_playground.R inst/doc/EuPathDB_trey_playground.Rmd inst/doc/reference.pdf inst/exporting_data_web_services.pdf inst/reference.pdf inst/scripts/config.R inst/scripts/make-data.R inst/scripts/make-data_amoebadb.R inst/scripts/make-data_cryptodb.R inst/scripts/make-data_fungidb_evens.R inst/scripts/make-data_fungidb_odds.R inst/scripts/make-data_giardiadb.R inst/scripts/make-data_microsporidiadb.R inst/scripts/make-data_piroplasmodb.R inst/scripts/make-data_plasmodb_evens.R inst/scripts/make-data_plasmodb_odds.R inst/scripts/make-data_schistodb.R inst/scripts/make-data_toxodb.R inst/scripts/make-data_trichdb.R inst/scripts/make-data_tritrypdb_evens.R inst/scripts/make-data_tritrypdb_odds.R inst/scripts/make_data.Rmd man/EuPathDB.Rd man/build.Rd man/build_dir.Rd man/check_csv.Rd man/check_files.Rd man/check_post_result.Rd man/check_rda.Rd man/check_s3.Rd man/choose_successful_post.Rd man/clean_pkg.Rd man/copy_s3_file.Rd man/download_eupath_metadata.Rd man/error.Rd man/extract_eupath_orthologs.Rd man/extract_gene_locations.Rd man/get_all_metadata.Rd man/get_eupath_entry.Rd man/get_eupath_pkgnames.Rd man/get_kegg_orgn.Rd man/get_metadata_filename.Rd man/get_rda_filename.Rd man/get_semantic_columns.Rd man/get_versions.Rd man/grapes-colon-colon-colon-grapes.Rd man/info.Rd man/kegg_vector_to_df.Rd man/load_ah_annotations.Rd man/load_eupath_annotations.Rd man/load_eupath_go.Rd man/load_eupath_pkg.Rd man/load_kegg_annotations.Rd man/load_orgdb_annotations.Rd man/load_orgdb_go.Rd man/make_eupath_bsgenome.Rd man/make_eupath_granges.Rd man/make_eupath_organismdbi.Rd man/make_eupath_orgdb.Rd man/make_eupath_txdb.Rd man/make_get_query.Rd man/make_post_attempts.Rd man/make_taxon_names.Rd man/move_final_package.Rd man/orgdb_from_ah.Rd man/pipe.Rd man/post_eupath_annotations.Rd man/post_eupath_go_table.Rd man/post_eupath_goslim_table.Rd man/post_eupath_interpro_table.Rd man/post_eupath_linkout_table.Rd man/post_eupath_ortholog_table.Rd man/post_eupath_pathway_table.Rd man/post_eupath_pdb_table.Rd man/post_eupath_pubmed_table.Rd man/post_eupath_table.Rd man/prefix_map.Rd man/print.downloaded_metadata.Rd man/query_s3_ah.Rd man/query_s3_file.Rd man/query_s3_granges.Rd man/query_s3_orgdb.Rd man/query_s3_txdb.Rd man/remove_eupath_nas.Rd man/search_na_taxon.Rd man/sm.Rd man/warn.Rd man/write_eupath_metadata.Rd man/xref_ah_species.Rd man/xref_gidb_species.Rd man/xref_taxonomy_number.Rd tests/testthat.R tests/testthat/test_001_metadata_tritrypdb.R tests/testthat/test_002_metadata_fungidb.R tests/testthat/test_010_orgdb_tritrypdb.R tests/testthat/test_011_txdb_tritrypdb.R tests/testthat/test_012_granges_tritrypdb.R tests/testthat/test_013_bsgenome_tritrypdb.R tests/testthat/test_014_organismdbi_tritrypdb.R tests/testthat/test_020_orgdb_fungidb.R tests/testthat/test_021_txdb_fungidb.R tests/testthat/test_022_granges_fungidb.R tests/testthat/test_030_leishmania_panamensis_mhomcol.R tests/testthat/test_030_schizosaccharomyces_pombe.R tests/testthat/test_042_fungidb_orgdb.R tests/testthat/test_043_giardiadb_orgdb.R tests/testthat/test_044_microsporidiadb_orgdb.R tests/testthat/test_045_piroplasmadb_orgdb.R tests/testthat/test_046_plasmodb_orgdb.R tests/testthat/test_047_toxodb_orgdb.R tests/testthat/test_048_trichdb_orgdb.R tests/testthat/test_049_tritrypdb_orgdb.R tests/testthat/test_059_tritrypdb_txdb.R tests/testthat/test_069_tritrypdb_bsgenome.R vignettes/EuPathDB_AnnotationHub_Tutorial.Rmd vignettes/EuPathDB_Developers_Guide.Rmd vignettes/EuPathDB_Package_Generation_Tutorial.Rmd vignettes/EuPathDB_trey_playground.Rmd