rentrez (version 1.2.3)

'Entrez' in R

Description

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.

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Install

install.packages('rentrez')

Monthly Downloads

17,498

Version

1.2.3

License

MIT + file LICENSE

Issues

Pull Requests

Stars

196

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Repository

https://docs.ropensci.org/rentrez/ (website) https://github.com/ropensci/rentrez/

Maintainer

David Winter

Last Published

November 10th, 2020

Functions in rentrez (1.2.3)

entrez_db_links

List available links for records from a given NCBI database

entrez_citmatch

Fetch pubmed ids matching specially formatted citation strings

entrez_link

Get links to datasets related to records from an NCBI database

entrez_global_query

Find the number of records that match a given term across all NCBI Entrez databases

entrez_dbs

List databases available from the NCBI

entrez_db_searchable

List available search fields for a given database

entrez_post

Post IDs to Eutils for later use

entrez_db_summary

Retrieve summary information about an NCBI database

entrez_fetch

Download data from NCBI databases

entrez_info

Get information about EUtils databases

parse_pubmed_xml

Summarize an XML record from pubmed.

set_entrez_key

Set the ENTREZ_KEY variable to be used by all rentrez functions

rentrez

entrez_summary

Get summaries of objects in NCBI datasets from a unique ID

entrez_search

Search the NCBI databases using EUtils

linkout_urls

Extract URLs from an elink object

extract_from_esummary

Extract elements from a list of esummary records