Package: reutils 0.2.5

reutils: 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.

Authors:Gerhard Schöfl <[email protected]>

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reutils.pdf |reutils.html✨
reutils/json (API)
NEWS

# Install 'reutils' in R:

install.packages('reutils', repos = c('https://gschofl.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/gschofl/reutils/issues

On CRAN:

26 exports 20 stars 2.42 score 15 dependencies 1 dependents 2 mentions 144 scripts 830 downloads

Last updated 4 years agofrom:68854991f8. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 06 2024
R-4.5-win	NOTE	Sep 06 2024
R-4.5-linux	NOTE	Sep 06 2024
R-4.4-win	NOTE	Sep 06 2024
R-4.4-mac	NOTE	Sep 06 2024
R-4.3-win	NOTE	Sep 06 2024
R-4.3-mac	NOTE	Sep 06 2024

Exports:content database ecitmatch efetch egquery einfo elink epost esearch espell esummary getError getUrl linkset make_flattener ncbi_retrieval_type performQuery querykey retmode rettype uid webenv xattr xname xset xvalue

Dependencies:assertthat cli curl fansi glue jsonlite lifecycle magrittr pillar pkgconfig rlang tibble utf8 vctrs XML

Introduction to reutils

Gerhard Schöfl

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Sep 06 2024.

Last update: 2020-10-08
Started: 2018-12-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
reutils: Talk to the NCBI EUtils	reutils-package reutils
EFetch accessors	[,efetch,character,missing-method [[,efetch,character-method
EInfo accessors	[,einfo,ANY,missing-method [[,einfo,ANY-method
ELink Accessors	[,elink,ANY,missing-method [,elink,character,ANY-method
ESearch Accessors	[,esearch,numeric,missing-method
ESummary accessors	[,esummary,character,ANY-method [[,esummary,character-method
Extract the data content from an Entrez request	content content,ecitmatch-method content,efetch-method content,egquery-method content,einfo-method content,elink-method content,epost-method content,esearch-method content,espell-method content,esummary-method content,eutil-method
database	database database,entrez_linkset-method database,entrez_uid-method database,eutil-method
ecitmatch - searching PubMed with citation data	ecitmatch
efetch - downloading full records	efetch
egquery - performing a global Entrez search	egquery
einfo - getting database statistics and search fields	einfo
elink - finding related data through Entrez links	elink
epost - uploading UIDs to Entrez	epost
esearch - searching an Entrez database	esearch
espell - retrieving spelling suggestions	espell
esummary - downloading Document Summaries	esummary
getError	getError getError,eutil-method
getUrl	getUrl getUrl,eutil-method
linkset	linkset linkset,elink-method linkset,entrez_linkset-method
querykey	querykey querykey,entrez_uid-method querykey,epost-method querykey,esearch-method
retmode	retmode retmode,eutil-method
rettype	rettype rettype,eutil-method
uid	uid uid,elink-method uid,entrez_linkset-method uid,entrez_uid-method uid,esearch-method
webenv	webenv webenv,entrez_uid-method webenv,epost-method webenv,esearch-method