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.
| Author | David Winter [aut, cre], Scott Chamberlain [ctb], Han Guangchun [ctb] |
| Date of publication | 2016-10-26 10:37:53 |
| Maintainer | David Winter <david.winter@gmail.com> |
| License | MIT + file LICENSE |
| Version | 1.0.4 |
| URL | http://github.com/ropensci/rentrez |
| Package repository | View on CRAN |
| Installation | Install the latest version of this package by entering the following in R:
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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 | |
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inst
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inst/doc
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| inst/doc/rentrez_tutorial.R | |
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inst/doc/rentrez_tutorial.html
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| inst/doc/rentrez_tutorial.Rmd | |
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tests
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tests/testthat
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| 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 | |
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NAMESPACE
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NEWS
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R
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| 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 | |
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vignettes
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| vignettes/rentrez_tutorial.Rmd | |
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MD5
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build
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build/vignette.rds
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DESCRIPTION
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man
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| 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 | |
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LICENSE
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