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DESCRIPTION
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DESCRIPTION
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Package: EuPathDB
Title: Provides access to pathogen annotation resources available on EuPathDB databases
Version: 1.6.0
Author: Keith Hughitt, Ashton Trey Belew
Authors@R: c(person("Keith", "Hughitt", email="khughitt@umd.edu", role=c("aut","cre")),
person("Ashton", "Belew", email="abelew@gmail.com", role=c("aut")))
Maintainer: Keith Hughitt <khughitt@umd.edu>
Description: Brings together annotation resources from the various EuPathDB
databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them
available in R using the AnnotationHub framework.
Depends:
R (>= 3.5),
GenomeInfoDbData,
Imports: AnnotationHub, AnnotationHubData,
Biobase, Biostrings, BiocGenerics,
data.table, dplyr,
foreach,
GenomeInfoDb, GenomicRanges, glue,
httr,
jsonlite,
magrittr,
readr, rtracklayer, rvest,
utils,
xml2
Suggests:
AnnotationDbi, AnnotationForge,
BiocManager, BiocStyle, BSgenome,
curl,
desc, devtools,
GenomicFeatures, GO.db,
KEGGREST, knitr,
OrganismDbi,
RCurl, reactome.db, RSQLite,
S4Vectors, stringr, testthat, tidyr
biocViews: AnnotationData, AnnotationHub, DataImport, EuPathDB
License: Artistic-2.0
URL: https://github.com/khughitt/EuPathDB
BugReports: https://github.com/khughitt/EuPathDB/issues
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Collate:
'check_csv.R'
'check_files.R'
'check_rda.R'
'check_s3.R'
'clean_pkg.R'
'copy_s3_file.R'
'download_eupath_metadata.R'
'eupathdb.R'
'expand_list_columns.R'
'extract_eupath_orthologs.R'
'extract_gene_locations.R'
'get_all_metadata.R'
'get_eupath_annotation_columns.R'
'get_eupath_entry.R'
'get_eupath_gene_types.R'
'get_eupath_pkgnames.R'
'get_kegg_orgn.R'
'get_metadata_filename.R'
'get_semantic_columns.R'
'get_tags.R'
'kegg_vector_to_df.R'
'get_versions.R'
'load_ah_annotations.R'
'load_eupath_annotations.R'
'load_eupath_go.R'
'load_eupath_pkg.R'
'load_kegg_annotations.R'
'load_orgdb_annotations.R'
'load_orgdb_go.R'
'logging.R'
'make_eupath_bsgenome.R'
'make_eupath_granges.R'
'make_eupath_organismdbi.R'
'make_eupath_orgdb.R'
'make_eupath_txdb.R'
'make_taxon_names.R'
'move_final_package.R'
'orgdb_from_ah.R'
'post_eupath_annotations.R'
'post_eupath_go.R'
'post_eupath_goslim.R'
'post_eupath_interpro.R'
'post_eupath_linkout.R'
'post_eupath_ortholog.R'
'post_eupath_pathway.R'
'post_eupath_pdb.R'
'post_eupath_pubmed.R'
'post_eupath_table.R'
'prefix_map.R'
'query_s3_file.R'
'query_s3_ah.R'
'remove_eupath_nas.R'
'test_helpers.R'
'write_eupath_metadata.R'
'xref_species.R'
'xref_taxonomy.R'
'zzz_print.R'