/
_pkgdown.yml
125 lines (123 loc) · 2.57 KB
/
_pkgdown.yml
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destination: working
reference:
- title: Set-up
desc: Set and verify your restez path
contents:
- restez_path_set
- restez_path_get
- restez_path_unset
- restez_connect
- restez_disconnect
- restez_status
- restez_ready
- title: Database
desc: Download, create, delete and verify your local database
contents:
- db_create
- db_delete
- db_download
- demo_db_create
- is_in_db
- list_db_ids
- count_db_ids
- ncbi_acc_get
- print.status
- title: GenBank
desc: Retrieve data from the local GenBank database
contents:
- gb_definition_get
- gb_fasta_get
- gb_organism_get
- gb_record_get
- gb_sequence_get
- gb_version_get
- gb_extract
- title: Entrez wrappers
desc: Wrappers for integration with the R package rentrez
contents:
- entrez_fetch
- title: Data
desc: Example data
contents:
- record
- title: Internal functions
desc: Private internal functions, documented here for openness
contents:
- add_rcrd_log
- cat_line
- char
- check_connection
- cleanup
- connected
- connection_get
- db_download_intern
- db_sqlngths_get
- db_sqlngths_log
- dir_size
- dwnld_path_get
- dwnld_rcrd_log
- entrez_fasta_get
- entrez_gb_get
- extract_accession
- extract_by_patterns
- extract_by_patterns
- extract_clean_sequence
- extract_definition
- extract_features
- extract_inforecpart
- extract_keywords
- extract_locus
- extract_organism
- extract_seqrecpart
- extract_sequence
- extract_version
- file_download
- filename_log
- flatfile_read
- gb_build
- gb_df_create
- gb_df_generate
- gb_sql_add
- gb_sql_query
- gbrelease_check
- gbrelease_get
- gbrelease_log
- has_data
- identify_downloadable_files
- last_add_get
- last_dwnld_get
- last_entry_get
- latest_genbank_release
- latest_genbank_release
- latest_genbank_release_notes
- latest_genbank_release_notes
- message_missing
- mock_def
- mock_gb_df_generate
- mock_org
- mock_rec
- mock_seq
- predict_datasizes
- readme_log
- restez_path_check
- restez_rl
- search_gz
- seshinfo_log
- setup
- slctn_get
- slctn_log
- sql_path_get
- stat
- status_class
- testdatadir_get
articles:
- title: All articles
navbar: ~
desc: Detailed tutorials for using `restez`
contents:
- restez
- '`1_rodents`'
- '`2_search_and_fetch`'
- '`3_parsing`'
- '`4_phylotar`'
- '`5_tips_and_tricks`'