Talk to the NCBI EUtils

An interface to NCBI databases such as PubMed, GenBank, or GEO powered by the Entrez Programming Utilities (EUtils). The nine EUtils provide programmatic access to the NCBI Entrez query and database system for searching and retrieving biological data.


reutils 0.2.3

  • content(x, 'parsed') returns tibbles instead of data.frames where approbriate.
  • Change base URLs for NCBI services to use https instead of http (#7).
  • Correctly return the first esummary record from an epost (#6).

reutils 0.2.2

  • Correctly print empty LinkSets (#5).

reutils 0.2.1

  • Updated URLs in documentation (#4).
  • New parameters 'version' and 'retmode' in einfo().
  • New parameters 'sort' and 'retmode' in esearch().
  • New parameter 'retmode' in esummary().
  • Support for JSON as alternative output format for EInfo, ESearch and ESummary.
  • Allow batch download to file for more than 500 records in efetch() (#2).
  • Correctly return hit count in esearch() if rettype = "count" (#3).

reutils 0.1.2

  • Add global option reutils.test.remote to control if unit tests that require online access to NCBI EUtilities are run or not.

reutils 0.1.1

  • Add global option to control the number of head lines displayed in show,efetch method (currently only if rettype = "text".

  • new return type content(x, as = "textConnection").

Reference manual

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0.2.3 by Gerhard Schöfl, 5 years ago

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Browse source code at

Authors: Gerhard Schöfl <[email protected]>

Documentation:   PDF Manual  

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MIT + file LICENSE license

Imports assertthat, jsonlite, methods, RCurl, stats, XML, tibble

Suggests testthat

Suggested by disprose.

See at CRAN