rentrez: Entrez in R
Version 1.0.4

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.

AuthorDavid Winter [aut, cre], Scott Chamberlain [ctb], Han Guangchun [ctb]
Date of publication2016-10-26 10:37:53
MaintainerDavid Winter <david.winter@gmail.com>
LicenseMIT + file LICENSE
Version1.0.4
URL http://github.com/ropensci/rentrez
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("rentrez")

Getting started

Rentrez Tutorial

Popular man pages

entrez_dbs: List databases available from the NCBI
entrez_db_searchable: List available search fields for a given database
entrez_db_summary: Retrieve summary information about an NCBI database
entrez_global_query: Find the number of records that match a given term across all...
entrez_link: Get links to datasets related to records from an NCBI...
entrez_search: Search the NCBI databases using EUtils
parse_pubmed_xml: Summarize an XML record from pubmed.
See all...

All man pages Function index File listing

Man pages

entrez_citmatch: Fetch pubmed ids matching specially formatted citation...
entrez_db_links: List available links for records from a given NCBI database
entrez_dbs: List databases available from the NCBI
entrez_db_searchable: List available search fields for a given database
entrez_db_summary: Retrieve summary information about an NCBI database
entrez_fetch: Download data from NCBI databases
entrez_global_query: Find the number of records that match a given term across all...
entrez_info: Get information about EUtils databases
entrez_link: Get links to datasets related to records from an NCBI...
entrez_post: Post IDs to Eutils for later use
entrez_search: Search the NCBI databases using EUtils
entrez_summary: Get summaries of objects in NCBI datasets from a unique ID
extract_from_esummary: Extract elements from a list of esummary records
linkout_urls: Extract URLs from an elink object
parse_pubmed_xml: Summarize an XML record from pubmed.
rentrez: rentrez

Functions

add_class Source code
as.data.frame.eInfoList Source code
check_json_errs Source code
check_xml_errors Source code
entrez_check Source code
entrez_citmatch Man page Source code
entrez_db_links Man page Source code
entrez_db_searchable Man page Source code
entrez_db_summary Man page Source code
entrez_dbs Man page Source code
entrez_email Source code
entrez_fetch Man page Source code
entrez_global_query Man page Source code
entrez_info Man page Source code
entrez_link Man page Source code
entrez_post Man page Source code
entrez_search Man page Source code
entrez_summary Man page Source code
entrez_tool Source code
extract_from_esummary Man page Source code
extract_from_esummary.esummary Source code
extract_from_esummary.esummary_list Source code
extract_pmid Source code
get_linked_elements Source code
id_or_webenv Source code
is_xml_record Source code
last Source code
linkout_urls Man page Source code
make_elink_fxn Source code
make_entrez_query Source code
parse_acheck Source code
parse_check Source code
parse_elink Source code
parse_esearch Source code
parse_esearch.XMLInternalDocument Source code
parse_esearch.list Source code
parse_esumm_int Source code
parse_esumm_list Source code
parse_esummary Source code
parse_esummary.XMLInternalDocument Source code
parse_esummary.list Source code
parse_history Source code
parse_linkouts Source code
parse_neighbors Source code
parse_node Source code
parse_one_pubmed Source code
parse_pubmed_xml Man page Source code
parse_response Source code
print.eInfoEntry Source code
print.eInfoLink Source code
print.eInfoSearch Source code
print.elink Source code
print.elink_classic Source code
print.elink_list Source code
print.esearch Source code
print.esummary Source code
print.esummary_list Source code
print.linkout Source code
print.multi_pubmed_record Source code
print.pubmed_record Source code
print.web_history Source code
rentrez Man page
rentrez-package Man page
web_history Source code

Files

inst
inst/doc
inst/doc/rentrez_tutorial.R
inst/doc/rentrez_tutorial.html
inst/doc/rentrez_tutorial.Rmd
tests
tests/testthat
tests/testthat/test_search.r
tests/testthat/test_query.r
tests/testthat/test_citmatch.r
tests/testthat/test_summary.r
tests/testthat/test_post.r
tests/testthat/test_docs.r
tests/testthat/test_net.r
tests/testthat/test_httr.r
tests/testthat/test_webenv.r
tests/testthat/test_parse.r
tests/testthat/test_fetch.r
tests/testthat/test_link.r
tests/testthat/test_info.r
tests/test-all.R
NAMESPACE
NEWS
R
R/entrez_global_query.r
R/base.r
R/entrez_citmatch.r
R/parse_pubmed_xml.r
R/entrez_search.r
R/entrez_info.r
R/help.r
R/entrez_link.r
R/entrez_fetch.r
R/entrez_summary.r
R/entrez_post.r
vignettes
vignettes/rentrez_tutorial.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/entrez_dbs.Rd
man/entrez_db_searchable.Rd
man/entrez_db_links.Rd
man/entrez_link.Rd
man/entrez_post.Rd
man/entrez_summary.Rd
man/entrez_db_summary.Rd
man/parse_pubmed_xml.Rd
man/entrez_info.Rd
man/linkout_urls.Rd
man/entrez_fetch.Rd
man/rentrez.Rd
man/entrez_global_query.Rd
man/entrez_search.Rd
man/extract_from_esummary.Rd
man/entrez_citmatch.Rd
LICENSE
rentrez documentation built on May 20, 2017, 12:53 a.m.

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