Package: epigraphdb 0.2.3

Yi Liu

epigraphdb: Interface Package for the 'EpiGraphDB' Platform

The interface package to access data from the 'EpiGraphDB' <https://epigraphdb.org> platform. It provides easy access to the 'EpiGraphDB' platform with functions that query the corresponding REST endpoints on the API <https://api.epigraphdb.org> and return the response data in the 'tibble' data frame format.

Authors:Yi Liu [cre, aut], Valeriia Haberland [aut], Marina Vabistsevits [aut], Tom Gaunt [aut], MRC IEU [cph]

epigraphdb_0.2.3.tar.gz
epigraphdb_0.2.3.zip(r-4.7)epigraphdb_0.2.3.zip(r-4.6)epigraphdb_0.2.3.zip(r-4.5)
epigraphdb_0.2.3.tgz(r-4.6-any)epigraphdb_0.2.3.tgz(r-4.5-any)
epigraphdb_0.2.3.tar.gz(r-4.7-any)epigraphdb_0.2.3.tar.gz(r-4.6-any)
epigraphdb_0.2.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
epigraphdb/json (API)

# Install 'epigraphdb' in R:
install.packages('epigraphdb', repos = c('https://mrcieu.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mrcieu/epigraphdb-r/issues

Pkgdown/docs site:https://mrcieu.github.io

On CRAN:

Conda:

api-clientbioinformaticsepidemiologygraph-databasemendelian-randomizationphenotypes

6.20 score 31 stars 17 scripts 315 downloads 23 exports 19 dependencies

Last updated from:1cd05d8426. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK155
source / vignettesOK208
linux-release-x86_64OK157
macos-release-arm64OK100
macos-oldrel-arm64OK82
windows-develOK85
windows-releaseOK77
windows-oldrelOK98
wasm-releaseOK139

Exports:%>%confoundercypherdrugs_risk_factorsgenetic_corliterature_gwasmappings_gene_to_proteinmeta_nodes_listmeta_nodes_list_nodemeta_nodes_search_nodemeta_rels_listmeta_rels_list_relmrobs_corontology_gwas_efopathwaypqtlpqtl_listpqtl_pleioprotein_in_pathwayquery_epigraphdbxqtl_multi_snp_mrxqtl_single_snp_mr

Dependencies:askpassclicurlgluehttrjsonlitelifecyclemagrittrmimeopensslpillarpkgconfigpurrrR6rlangsystibbleutf8vctrs

About
EpiGraphDB resources
Rendered fromabout.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2019-11-10

Getting started with EpiGraphDB in R
Part 1: Using EpiGraphDB to obtain biological mappings | Mapping genes to proteins | Mapping proteins to pathways | Get pathway info | Part 2: Epidemiological relationships analysis | Look up GWAS studies | Explore Mendelian randomization studies | Specify exposure trait | Specify outcome trait | Specify both exposure and outcome traits | Part 3. Looking for literature evidence | EpiGraphDB node search | Advanced examples
Rendered fromgetting-started-with-epigraphdb-r.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2020-09-29

Meta functionalities of the EpiGraphDB platform
Metadata | Meta nodes | Meta relationships and connections | Search for specific node | Fuzzy matching | Exact matching | Cypher (advanced) | sessionInfo
Rendered frommeta-functionalities.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2020-06-01

Options
Change the API URL | Suppress start up message
Rendered fromoptions.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2019-11-11

Using EpiGraphDB API
Introduction | Using httr | Using curl | Other methods
Rendered fromusing-epigraphdb-api.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2019-11-10

Using EpiGraphDB R package
Methods to query EpiGraphDB | mr | GET /mr | Returned data format | mode = "table" | mode = "raw"
Rendered fromusing-epigraphdb-r-package.Rmdusingknitr::rmarkdown

Last update: 2022-01-14
Started: 2019-07-04