Package index
-
DO_colors
- Human Disease Ontology Official Colors
-
DOrepo()
- Instantiate a DO Repository
-
all_duplicated()
- Identify all duplicates
-
append_empty_col()
- Append Empty Columns
-
append_to_url()
- Append to URL
-
as_tibble(<esummary_list>)
as_tibble(<esummary_list_nested>)
- Convert
esummary
Object into Tibble
-
as_tibble(<scopus_search>)
as_tibble(<scopus_search_list>)
- Convert
scopus_search
Object into Tibble
-
batch_id_converter()
- Convert IDs in Batches
-
build_hyperlink()
- Build Hyperlinks
-
is_blank()
is_missing()
- Character value predicates
-
partition()
- Partition vectors
-
citedby_pmid()
- Get Cited By PMIDs from PubMed
-
citedby_pubmed()
- Get Cited By List from PubMed
-
citedby_scopus()
- Get Cited By List from Scopus
-
collapse_col()
- Collapse Column(s)
-
collapse_col_flex()
- Collapse Column(s) Flexibly
-
collapse_to_string()
- Create a String from Inputs
-
confine_list()
release_list()
- Convert (Nested) List to/from Character Vector
-
count_alliance_records()
- Count Alliance Records
-
count_delim()
- Count Delimited Columns
-
cur_yr()
- Get Current Year
-
download_alliance_tsv()
- Download Alliance .tsv.gz File
-
download_file()
- Download File(s) from the Internet
-
download_obo_ontology()
- Download OBO Foundry Ontology File
-
download_omim()
- Download OMIM Files
-
drop_blank()
- Drop Blanks
-
elucidate()
- Elucidate the Data in an Object
-
extract_as_tidygraph()
- Extract OWL/RDF as a tidygraph
-
extract_class_axiom()
- Extract Class Axioms
-
extract_eq_axiom()
- Extract Equivalent Class Axioms
-
extract_ordo_mappings()
- Extract mappings from ORDO
-
extract_pm_date()
- Extract Publication Date from PubMed Citations
-
extract_pmid()
- Extract PubMed ID
-
extract_pmid(<elink>)
- Extract PubMed ID from elink object
-
extract_pmid(<elink_list>)
- Extract PubMed ID from elink_list object
-
extract_subclass_axiom()
- Extract 'Subclass Of' Axioms
-
extract_subtree()
- Extract Subtree
-
format_axiom()
- Format Logical Axioms
-
format_doid()
- Format DOIDs
-
format_hyperlink()
- Format URLs as Hyperlinks
-
format_obo()
- Format OBO Foundry IDs
-
format_subtree()
- Format a Subtree
-
get_bioc_pkg_stats()
- Get Bioconductor Package Statistics
-
iff_all_vals()
- Test for All Values
-
install_robot()
- Install OBO Foundry ROBOT Tool (Mac/Linux ONLY)
-
inventory_omim()
- Assess whether OMIM Data is in DO
-
invert_sublists()
- Invert Sublists
-
is_curie()
- CURIE (RDF ID) Predicate
-
is_invariant()
- Test if an Object is Invariant
-
length_sort()
length_order()
- Sort by Character Length
-
lengthen_col()
- Lengthen Column(s)
-
lexiclean()
- Prepare Text for Matching
-
is_boolean()
- Logical predicate
-
make_contributor_html()
- Make "Contributors" HTML
-
make_use_case_html()
- Make HTML for DO Use Case Tables
-
make_user_list_html()
- Make HTML for DO User List (DEPRECATED)
-
match_carefully()
- Matches Carefully
-
match_citations()
- Citation Matching
-
match_fz()
- Fuzzy (Approximate) String Matching
-
ns_prefix
obo_prefix
obo_prop_prefix
not_obo_prefix
- Namespace Prefixes
-
is_positive()
is_negative()
is_whole_number()
is_scalar_whole_number()
- Number value predicates
-
is_valid_obo()
is_valid_doid()
- OBO ID predicates
-
obofoundry_metadata
- OBO Foundry Metadata
-
onto_missing()
- Identify Data Missing from an Ontology (DEPRECATED)
-
owl_xml()
- Instantiate an owl_xml object
-
parse_mapping()
- Parse Mapping
-
plot_branch_counts()
- Plot Branch Counts
-
plot_citedby()
- Plot Publications Citing DO by Year
-
plot_def_src()
- Plot Definition Sources
-
plot_term_def_counts()
- Plot DO Term & Definition Counts
-
plot_xref_counts()
- Plot Xref Counts
-
pmc_summary()
- Get PubMed Central Summary
-
print(<oieb>)
- Print OMIM inventory report statistics
-
priority_sort()
- Sort Vectors by Priority
-
progress_bar-class
progress_bar
- Progress Bar (RefClass)
-
pub_id_match
- Prioritized List of Publication IDs & Regex's for Matching
-
pubmed_summary()
- Get PubMed Summary
-
pyDOID
- pyDOID
-
pyobo_map()
- Map Terms to Terms of Specified Namespace
-
queue_xref_split()
- Curation Queue: DOIDs to split?
-
read_alliance()
- Read Alliance .tsv.gz File
-
read_ga()
- Read Google Analytics Exports
-
read_omim()
- Read OMIM Data
-
read_pubmed_txt()
- Read in PubMed Citations (from txt file)
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replace_blank()
- Replace Blanks with Specified Value
-
replace_na(<list>)
- [DEPRECATED] Replace NAs with specified value
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replace_null()
- Replace NULLs with specified value
-
restore_names()
- Restore Element Names
-
robot()
- Execute Robot Commands
-
robot_query()
- Execute a SPARQL Query with ROBOT
-
round_down()
- Round Number Down
-
round_up()
- Round Number Up
-
round_zero()
- Round Number to Zero
-
sandwich_text()
- Sandwich Text Between Placeholders
-
save_alliance_counts()
- Writes Alliance Counts to File
-
search_pmc()
- Search PubMed Central
-
search_pubmed()
- Search PubMed
-
set_scopus_keys()
- Set Keys for Scopus API Access
-
suggest_regex()
- Suggest a Regular Expression That Will Match All Input
-
theme_DO()
- DO Theme for Stats Plots
-
tidy_pub_records()
- Tidy Publication Records
-
tidy_pubmed_summary()
- Convert PubMed summary to tibble (DEPRECATED)
-
tidy_sparql()
- Tidy SPARQL Query
-
to_curie()
- Convert URI to CURIE
-
to_range()
- Convert Vectors to Range String
-
to_uri()
- Convert CURIE to URI
-
today_datestamp()
- Today's Date Stamp
-
unique_if_invariant()
- Return Unique Value for Invariant Vectors
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unnest_cross()
- Unnest data frame list columns
-
unnest_mapping()
- Unnest Mapping
-
update_website_count_tables()
- Update Counts in DO Website HTML
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vctr_to_string()
unique_to_string()
- Convert Vectors to Strings
-
wrap_onscreen()
- Wrap an On-screen Message
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write_graphml()
- Write a Graph to .graphml File
-
write_gs()
- Write Data to a Google Sheet