Entrez in R

Provides an R interface to the NCBI's EUtils API allowing users to search databases like GenBank and PubMed, process the results of those searches and pull data into their R sessions.


Update to only use https * NCBI is goinh all https, rentrez will only use https from now on. * Added links to repo/bug reporting to DESCRIPTION * Documented changes to sequence database XML records * Allow automatic parsing of XML flavours

Bug fix release * Tests now work with testthat 1.0.0 * All calls to ncbi specify encoding is UTF-8 (saving error messages) * HTTP Error codes associated with large requests now give the user a hint to check out the documentation for web-history features

Bug fix release * Properly format "by_id" mode URLS (bug exposed by httr 1.0.1) * Handle case in which some IDs passed to "by_id" mode are invalide (thanks Zachary Foster for report) * Documentation updated to reflect OMIM->SNP links no longer possible * Use Rmarkdown (not knitr) as vignette builder * Return NCBI error messages are text when they exist

* new function extract_from_esummary() for extracting like-named elements
  from a list esummary records (e.g. get all "Title" fields from a list of 
  PubMed esummaries)
* Support for `cmd` option in entrez_link (breaks backward compatibility)
    * Allows discovery of external links from and use of web_history
    * New helper function linkout_urls to get URLs form external links
* Support for 'by_id' mode for entrez_link. Pass a vector of IDs to
  entrez_link, (optionally) get a list on elink objects back (one per ID)
* New web_history object makes using NCBI Web History features easier
* All of these changes documented in new vignette
* Han Guangchun added as contributor for his pull requests 
* New tests, minor bug fixes and extended documentation
  • Bug fix: The example for entrez_summary contained a typo which made it fail (being wrapped in dontest this hadn't previously shown up).
  • entrez_summary now fetches 'version 2.0' esummary records from NCBI
    • This change may break some scripts. In particular, the names of some elements in esummary records have changed. Broken scripts shold produce a helpful error message, and using entrez_summary(..., version="1.0") should fix it. More details are given in the help to entrez_summary.
    • When version 2.0 records are requested entrez_summary fetches the json record.
  • New helper functions for einfo Eutil
    • entrez_dbs() lists avaliable databases.
    • entrez_db_summary() gets summary information about a given database.
    • entrez_db_links() lists databases against which a given db's records might be cross referenced.
    • entrez_db_searchable() lists search terms avaliable for a given database.
  • Nicer print functions for search and summary objects
  • New dependancy on jsonlite for handling json records.
  • Bunch of bugs squashed and typos cleaned up
* Squashed a bug in the vignette which wrote to users $HOME
* using httr to handle HTTP GETs and some url building
* parsing for esummary parsing for clinvar database
* Scott Chamberlain added as contributer for above
* Pubmed parser handles multi-record files
* html vignette included
* minor release to fix bug in esummary parsing
* Edited license/description to meet CRAN requiremens
* Added sentence to description to summarise the package
* Parsing of esummary xmls is now much nicer. 
* S3 items to represent most results
* Tests to cover all functions
* First release on CRAN + now part of ROpenSci
* Functions cover the whole EUtils API

Reference manual

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1.1.0 by David Winter, 6 months ago


Report a bug at https://github.com/ropensci/rentrez/issues

Browse source code at https://github.com/cran/rentrez

Authors: David Winter [aut, cre], Scott Chamberlain [ctb], Han Guangchun [ctb]

Documentation:   PDF Manual  

Task views:

MIT + file LICENSE license

Imports XML, httr, jsonlite

Suggests testthat, knitr, rmarkdown

Imported by biolink, fulltext, rotl.

Suggested by BoSSA.

See at CRAN