rentrez: An R package for the NCBI eUtils API

By David J. Winter. The R Journal, 2017

295 citations recorded by the source corpus.

The USA National Center for Biotechnology Information (NCBI) is one of the world’s most important sources of biological information. NCBI databases like PubMed and GenBank contain millions of records describing bibliographic, genetic, genomic, and medical data. Here I present rentrez, a package which provides an R interface to 50 NCBI databases. The package is well-documented, contains an extensive suite of unit tests and has an active user base. The programmatic interface to the NCBI provided by rentrez allows researchers to query databases and download or import particular records into R sessions for subsequent analysis. The complete nature of the package, its extensive test-suite and the fact the package implements the NCBI’s usage policies all make rentrez a powerful aid to developers of new packages that perform more specific tasks.

Subfields: Ecological Modeling, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b1f442a2ff37d6fe52068fc51833e3d38e0376fd

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecological Modeling

1. E. Mächler
2. A. Alves
3. E. Batista
4. Anabela Lopes
5. F. Altermatt

In Molecular Biology

1. E. Mächler
2. A. Alves
3. E. Batista
4. J. Walser
5. Anabela Lopes
6. F. Altermatt

Citations in the corpus

• Assessing different components of diversity across a river network using eDNA (2019, methodology): “We used the R packages “taxize” (Chamberlain & Szöcs, 2013, version 0.9.7) and “rentrez” (Winter, 2017, version 1.2.2) to obtain taxonomic labels based on the ac‐ cession numbers.”
• What Do We Know about Botryosphaeriaceae? An Overview of a Worldwide Cured Dataset (2021, methodology): “An initial query was performed on 12-05-2020 in the Nucleotide—NCBI database using the search term “Botryosphaeriaceae [Organism]” with the R package rentrez [31].”
• Non‐specific amplification compromises environmental DNA metabarcoding with COI (2019, unknown): “1 (Winter, 2017) against NCBI 138 GenBank release 230 (nucleotide database; https://www.”