Showing 65 of total 65 results (show query)
r-dbi
DBI:R Database Interface
A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.
Maintained by Kirill Müller. Last updated 11 days ago.
302 stars 20.87 score 19k scripts 2.9k dependents
tidyverse
dbplyr:A 'dplyr' Back End for Databases
A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.
Maintained by Hadley Wickham. Last updated 4 months ago.
481 stars 19.72 score 5.2k scripts 736 dependentsr-dbi
RSQLite:SQLite Interface for R
Embeds the SQLite database engine in R and provides an interface compliant with the DBI package. The source for the SQLite engine and for various extensions in a recent version is included. System libraries will never be consulted because this package relies on static linking for the plugins it includes; this also ensures a consistent experience across all installations.
Maintained by Kirill Müller. Last updated 3 hours ago.
331 stars 18.78 score 8.1k scripts 1.1k dependentsr-dbi
odbc:Connect to ODBC Compatible Databases (using the DBI Interface)
A DBI-compatible interface to ODBC databases.
Maintained by Hadley Wickham. Last updated 2 days ago.
396 stars 16.31 score 2.9k scripts 23 dependentsr-dbi
RPostgres:C++ Interface to PostgreSQL
Fully DBI-compliant C++-backed interface to PostgreSQL <https://www.postgresql.org/>, an open-source relational database.
Maintained by Kirill Müller. Last updated 1 months ago.
338 stars 14.78 score 1.6k scripts 31 dependentstidyverse
blob:A Simple S3 Class for Representing Vectors of Binary Data ('BLOBS')
R's raw vector is useful for storing a single binary object. What if you want to put a vector of them in a data frame? The 'blob' package provides the blob object, a list of raw vectors, suitable for use as a column in data frame.
Maintained by Kirill Müller. Last updated 4 months ago.
45 stars 13.82 score 157 scripts 1.4k dependents
duckdb
duckdb:DBI Package for the DuckDB Database Management System
The DuckDB project is an embedded analytical data management system with support for the Structured Query Language (SQL). This package includes all of DuckDB and an R Database Interface (DBI) connector.
Maintained by Kirill Müller. Last updated 10 days ago.
159 stars 13.80 score 1.7k scripts 46 dependentsr-dbi
RMySQL:Database Interface and 'MySQL' Driver for R
Legacy 'DBI' interface to 'MySQL' / 'MariaDB' based on old code ported from S-PLUS. A modern 'MySQL' client written in 'C++' is available from the 'RMariaDB' package.
Maintained by Jeroen Ooms. Last updated 2 months ago.
209 stars 13.68 score 3.7k scripts 15 dependentsr-dbi
bigrquery:An Interface to Google's 'BigQuery' 'API'
Easily talk to Google's 'BigQuery' database from R.
Maintained by Hadley Wickham. Last updated 1 months ago.
520 stars 12.47 score 1.8k scripts 4 dependentsr-dbi
RMariaDB:Database Interface and MariaDB Driver
Implements a DBI-compliant interface to MariaDB (<https://mariadb.org/>) and MySQL (<https://www.mysql.com/>) databases.
Maintained by Kirill Müller. Last updated 1 months ago.
133 stars 12.20 score 792 scripts 10 dependents
apache
adbcdrivermanager:'Arrow' Database Connectivity ('ADBC') Driver Manager
Provides a developer-facing interface to 'Arrow' Database Connectivity ('ADBC') for the purposes of driver development, driver testing, and building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 11.39 score 73 scripts 6 dependents
openml
OpenML:Open Machine Learning and Open Data Platform
We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers. The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs. See <https://www.openml.org/guide/api> for more information.
Maintained by Giuseppe Casalicchio. Last updated 10 months ago.
arffbenchmarkingbenchmarking-suiteclassificationdata-sciencedatabasedatasetdatasetsmachine-learningmachine-learning-algorithmsopen-dataopen-scienceopendataopenmlopenscienceregressionreproducible-researchstatistics
97 stars 11.04 score 7.1k scripts
ropensci
rebird:R Client for the eBird Database of Bird Observations
A programmatic client for the eBird database (<https://ebird.org/home>), including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
Maintained by Sebastian Pardo. Last updated 2 months ago.
birdsbirdingebirddatabasedatabiologyobservationssightingsornithologyebird-apiebird-webservicesspocc
90 stars 10.43 score 73 scripts 6 dependents
malaria-atlas-project
malariaAtlas:An R Interface to Open-Access Malaria Data, Hosted by the 'Malaria Atlas Project'
A suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the 'Malaria Atlas Project' <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.
Maintained by Mauricio van den Berg. Last updated 8 months ago.
44 stars 9.10 score 118 scripts 3 dependentsropensci
elastic:General Purpose Interface to 'Elasticsearch'
Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java' Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' API (<https://www.elastic.co/elasticsearch/>), including functions for setting connection details to 'Elasticsearch' instances, loading bulk data, searching for documents with both 'HTTP' query variables and 'JSON' based body requests. In addition, 'elastic' provides functions for interacting with API's for 'indices', documents, nodes, clusters, an interface to the cat API, and more.
Maintained by Scott Chamberlain. Last updated 2 years ago.
databaseelasticsearchhttpapisearchnosqljavajsondocumentsdata-sciencedatabase-wrapperetl
247 stars 8.98 score 151 scripts 1 dependentsapache
adbcpostgresql:'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'PostgreSQL' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 8.83 score 1 scriptsapache
adbcsqlite:'Arrow' Database Connectivity ('ADBC') 'SQLite' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'SQLite' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 8.83 score 1 scriptsropensci
ckanr:Client for the Comprehensive Knowledge Archive Network ('CKAN') API
Client for 'CKAN' API (<https://ckan.org/>). Includes interface to 'CKAN' 'APIs' for search, list, show for packages, organizations, and resources. In addition, provides an interface to the 'datastore' API.
Maintained by Francisco Alves. Last updated 2 years ago.
databaseopen-datackanapidatadatasetapi-wrapperckan-api
98 stars 8.60 score 448 scripts 4 dependentsropensci
nodbi:'NoSQL' Database Connector
Simplified JSON document database access and manipulation, providing a common API across supported 'NoSQL' databases 'Elasticsearch', 'CouchDB', 'MongoDB' as well as 'SQLite/JSON1', 'PostgreSQL', and 'DuckDB'.
Maintained by Ralf Herold. Last updated 5 months ago.
databasemongodbelasticsearchcouchdbsqlitepostgresqlduckdbnosqljsondocuments
78 stars 8.36 score 28 scripts 1 dependentsr-dbi
DBItest:Testing DBI Backends
A helper that tests DBI back ends for conformity to the interface.
Maintained by Kirill Müller. Last updated 12 days ago.
24 stars 8.21 score 11 scripts
rfhb
ctrdata:Retrieve and Analyze Clinical Trials Data from Public Registers
A system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from four public registers, the 'European Union Clinical Trials Register' ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 'ClinicalTrials.gov' (<https://clinicaltrials.gov/> and also translating queries the retired classic interface), the 'ISRCTN' (<http://www.isrctn.com/>) and the 'European Union Clinical Trials Information System' ('CTIS', <https://euclinicaltrials.eu/>). Trial information is downloaded, converted and stored in a database ('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi'). Protocols, statistical analysis plans, informed consent sheets and other documents in registers associated with trials can also be downloaded. Other functions implement trial concepts canonically across registers, identify deduplicated records, easily find and extract variables (fields) of interest even from complex nested data as used by the registers, merge variables and update queries. The package can be used for monitoring, meta- and trend-analysis of the design and conduct as well as of the results of clinical trials across registers.
Maintained by Ralf Herold. Last updated 8 days ago.
clinical-dataclinical-researchclinical-studiesclinical-trialsctgovdatabaseduckdbmongodbnodbipostgresqlregistersqlitestudiestrial
45 stars 7.97 score 32 scriptsapache
adbcsnowflake:Arrow Database Connectivity ('ADBC') 'Snowflake' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'Snowflake' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 7.83 score 1 scriptsapache
adbcbigquery:'Arrow' Database Connectivity ('ADBC') 'BigQuery' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'BigQuery' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 7.83 score 1 scriptsapache
adbcflightsql:'Arrow' Database Connectivity ('ADBC') 'FlightSQL' Driver
Provides a developer-facing interface to the 'Arrow' Database Connectivity ('ADBC') 'FlightSQL' driver for the purposes of building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.
Maintained by Dewey Dunnington. Last updated 1 days ago.
421 stars 7.83 score 2 scriptsropensci
ruODK:An R Client for the ODK Central API
Access and tidy up data from the 'ODK Central' API. 'ODK Central' is a clearinghouse for digitally captured data using ODK <https://docs.getodk.org/central-intro/>. It manages user accounts and permissions, stores form definitions, and allows data collection clients like 'ODK Collect' to connect to it for form download and submission upload. The 'ODK Central' API is documented at <https://docs.getodk.org/central-api/>.
Maintained by Florian W. Mayer. Last updated 5 months ago.
databaseopen-dataodkapidatadatasetodataodata-clientodk-centralopendatakit
42 stars 7.73 score 57 scripts 1 dependentsropensci
rdataretriever:R Interface to the Data Retriever
Provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.
Maintained by Henry Senyondo. Last updated 8 months ago.
datadata-sciencedatabasedatasetsscience
46 stars 7.70 score 36 scripts
tidymodels
modeldb:Fits Models Inside the Database
Uses 'dplyr' and 'tidyeval' to fit statistical models inside the database. It currently supports KMeans and linear regression models.
Maintained by Max Kuhn. Last updated 1 years ago.
databasedbplyrdplyrggplot2modelingrlangsqltidyevalvisualization
79 stars 7.59 score 62 scriptsropensci
sofa:Connector to 'CouchDB'
Provides an interface to the 'NoSQL' database 'CouchDB' (<http://couchdb.apache.org>). Methods are provided for managing databases within 'CouchDB', including creating/deleting/updating/transferring, and managing documents within databases. One can connect with a local 'CouchDB' instance, or a remote 'CouchDB' databases such as 'Cloudant'. Documents can be inserted directly from vectors, lists, data.frames, and 'JSON'. Targeted at 'CouchDB' v2 or greater.
Maintained by Yaoxiang Li. Last updated 2 months ago.
couchdbdatabasenosqldocumentscloudantcouchdb-client
33 stars 7.51 score 54 scripts
dyfanjones
noctua:Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI' Interface)
Designed to be compatible with the 'R' package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws' <https://github.com/paws-r/paws> is used as a driver.
Maintained by Dyfan Jones. Last updated 12 months ago.
46 stars 7.48 score 58 scripts
bioc
CuratedAtlasQueryR:Queries the Human Cell Atlas
Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.
Maintained by Stefano Mangiola. Last updated 5 months ago.
assaydomaininfrastructurernaseqdifferentialexpressiongeneexpressionnormalizationclusteringqualitycontrolsequencingtranscriptiontranscriptomicsdatabaseduckdbhdf5human-cell-atlassingle-cellsinglecellexperimenttidyverse
90 stars 7.04 score 41 scriptsdyfanjones
RAthena:Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Designed to be compatible with the R package 'DBI' (Database Interface) when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>. To do this 'Python' 'Boto3' Software Development Kit ('SDK') <https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Maintained by Dyfan Jones. Last updated 1 years ago.
37 stars 6.99 score 38 scriptsropensci
arkdb:Archive and Unarchive Databases Using Flat Files
Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
Maintained by Carl Boettiger. Last updated 1 years ago.
archivingdatabasedbipeer-reviewed
79 stars 6.86 score 37 scripts
cboettig
neonstore:NEON Data Store
The National Ecological Observatory Network (NEON) provides access to its numerous data products through its REST API, <https://data.neonscience.org/data-api/>. This package provides a high-level user interface for downloading and storing NEON data products. Unlike 'neonUtilities', this package will avoid repeated downloading, provides persistent storage, and improves performance. 'neonstore' can also construct a local 'duckdb' database of stacked tables, making it possible to work with tables that are far to big to fit into memory.
Maintained by Carl Boettiger. Last updated 12 months ago.
databaseecologyneon-dataprovenance
9 stars 6.67 score 143 scripts 11 dependentsropensci
rcites:R Interface to the Species+ Database
A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
Maintained by Kevin Cazelles. Last updated 2 years ago.
api-clientcitesdatabaseendangered-speciestrade
14 stars 6.52 score 26 scripts
eurostat
restatapi:Search and Retrieve Data from Eurostat Database
Eurostat is the statistical office of the European Union and provides high quality statistics for Europe. Large set of the data is disseminated through the Eurostat database (<https://ec.europa.eu/eurostat/web/main/data/database>). The tools are using the REST API with the Statistical Data and Metadata eXchange (SDMX) Web Services (<https://wikis.ec.europa.eu/pages/viewpage.action?pageId=44165555>) to search and download data from the Eurostat database using the SDMX standard.
Maintained by Mátyás Mészáros. Last updated 2 months ago.
databaseeurostatfilteropen-dataretrieve-datasdmx
25 stars 6.34 score 146 scripts 1 dependents
inbo
inbodb:Connect to and Retrieve Data from Databases on the INBO Server
A bundle of functions to connect to and retrieve data from databases on the INBO server, with dedicated functions to query some of these databases.
Maintained by Els Lommelen. Last updated 1 months ago.
6.16 score 114 scripts 1 dependentsropensci
dwctaxon:Edit and Validate Darwin Core Taxon Data
Edit and validate taxonomic data in compliance with Darwin Core standards (Darwin Core 'Taxon' class <https://dwc.tdwg.org/terms/#taxon>).
Maintained by Joel H. Nitta. Last updated 8 months ago.
6 stars 6.13 score 28 scriptsropensci
bikedata:Download and Aggregate Data from Public Hire Bicycle Systems
Download and aggregate data from all public hire bicycle systems which provide open data, currently including 'Santander' Cycles in London, U.K.; from the U.S.A., 'Ford GoBike' in San Francisco CA, 'citibike' in New York City NY, 'Divvy' in Chicago IL, 'Capital Bikeshare' in Washington DC, 'Hubway' in Boston MA, 'Metro' in Los Angeles LA, 'Indego' in Philadelphia PA, and 'Nice Ride' in Minnesota; 'Bixi' from Montreal, Canada; and 'mibici' from Guadalajara, Mexico.
Maintained by Mark Padgham. Last updated 1 years ago.
bicycle-hire-systemsbike-hire-systemsbike-hirebicycle-hiredatabasebike-datapeer-reviewedcpp
81 stars 5.96 score 28 scripts
traitecoevo
austraits:Helpful functions to access the AusTraits database and wrangle data from other traits.build databases
`austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.
Maintained by Fonti Kar. Last updated 3 months ago.
22 stars 5.93 score 43 scripts 1 dependents
dleutnant
influxdbr:R Interface to InfluxDB
An R interface to the InfluxDB time series database <https://www.influxdata.com>. This package allows you to fetch and write time series data from/to an InfluxDB server. Additionally, handy wrappers for the Influx Query Language (IQL) to manage and explore a remote database are provided.
Maintained by Dominik Leutnant. Last updated 5 years ago.
databaseinfluxdbtidyversetimeseries
94 stars 5.90 score 28 scripts
edwindj
chunked:Chunkwise Text-File Processing for 'dplyr'
Data stored in text file can be processed chunkwise using 'dplyr' commands. These are recorded and executed per data chunk, so large files can be processed with limited memory using the 'LaF' package.
Maintained by Edwin de Jonge. Last updated 3 years ago.
167 stars 5.54 score 21 scripts
luckinet
arealDB:Harmonise and Integrate Heterogeneous Areal Data
Many relevant applications in the environmental and socioeconomic sciences use areal data, such as biodiversity checklists, agricultural statistics, or socioeconomic surveys. For applications that surpass the spatial, temporal or thematic scope of any single data source, data must be integrated from several heterogeneous sources. Inconsistent concepts, definitions, or messy data tables make this a tedious and error-prone process. 'arealDB' tackles those problems and helps the user to integrate a harmonised databases of areal data. Read the paper at Ehrmann, Seppelt & Meyer (2020) <doi:10.1016/j.envsoft.2020.104799>.
Maintained by Steffen Ehrmann. Last updated 2 months ago.
2 stars 5.41 score 15 scripts
nikolaus77
rocker:Database Interface Class
'R6' class interface for handling relational database connections using 'DBI' package as backend. The class allows handling of connections to e.g. PostgreSQL, MariaDB and SQLite. The purpose is having an intuitive object allowing straightforward handling of SQL databases.
Maintained by Nikolaus Pawlowski. Last updated 3 years ago.
databasedbimariadbmysqlpostgrespostgresqlr6sqlsqlite
5 stars 5.24 score 7 scripts
statistikat
STATcubeR:R Interface for the 'STATcube' REST API and Open Government Data
Import data from the 'STATcube' REST API or from the open data portal of Statistics Austria. This package includes a client for API requests as well as parsing utilities for data which originates from 'STATcube'. Documentation about 'STATcubeR' is provided by several vignettes included in the package as well as on the public 'pkgdown' page at <https://statistikat.github.io/STATcubeR/>.
Maintained by Bernhard Meindl. Last updated 4 months ago.
18 stars 5.03 score 9 scripts
ianmcook
queryparser:Translate 'SQL' Queries into 'R' Expressions
Translate 'SQL' 'SELECT' statements into lists of 'R' expressions.
Maintained by Ian Cook. Last updated 2 years ago.
54 stars 5.02 score 13 scripts 1 dependentsr-dbi
adbi:'DBI' Compliant Database Access Using 'ADBC'
In order to make Arrow Database Connectivity ('ADBC' <https://arrow.apache.org/adbc/>) accessible from R, an interface compliant with the 'DBI' package is provided, using driver back-ends that are implemented in the 'adbcdrivermanager' framework. This enables interacting with database systems using the Arrow data format, thereby offering an efficient alternative to 'ODBC' for analytical applications.
Maintained by Nicolas Bennett. Last updated 4 months ago.
17 stars 5.01 score 1 scripts
tomroh
bcputility:Wrapper for SQL Server bcp Utility
Provides functions to utilize a command line utility that does bulk inserts and exports from SQL Server databases.
Maintained by Thomas Roh. Last updated 8 months ago.
14 stars 4.99 score 28 scripts
psychbruce
ChineseNames:Chinese Name Database 1930-2008
A database of Chinese surnames and Chinese given names (1930-2008). This database contains nationwide frequency statistics of 1,806 Chinese surnames and 2,614 Chinese characters used in given names, covering about 1.2 billion Han Chinese population (96.8% of the Han Chinese household-registered population born from 1930 to 2008 and still alive in 2008). This package also contains a function for computing multiple features of Chinese surnames and Chinese given names for scientific research (e.g., name uniqueness, name gender, name valence, and name warmth/competence).
Maintained by Han-Wu-Shuang Bao. Last updated 2 years ago.
big-datachinesechinese-namechinese-namesdatabasenamenames
150 stars 4.88 score 6 scripts
mlr-org
mlr3db:Data Base Backend for 'mlr3'
Extends the 'mlr3' package with a backend to transparently work with databases such as 'SQLite', 'DuckDB', 'MySQL', 'MariaDB', or 'PostgreSQL'. The package provides two additional backends: 'DataBackendDplyr' relies on the abstraction of package 'dbplyr' to interact with most DBMS. 'DataBackendDuckDB' operates on 'DuckDB' data bases and also on Apache Parquet files.
Maintained by Michel Lang. Last updated 1 years ago.
bigquerydata-backenddatabaseduckdbmachine-learningmariadbmlr3mysqlodbcpostgresqlsparksqlite
21 stars 4.77 score 17 scripts
mcodrescu
octopus:A Database Management Tool
A database management tool built as a 'shiny' application. Connect to various databases to send queries, upload files, preview tables, and more.
Maintained by Marcus Codrescu. Last updated 12 months ago.
11 stars 4.74 score 4 scriptsbioc
brendaDb:The BRENDA Enzyme Database
R interface for importing and analyzing enzyme information from the BRENDA database.
Maintained by Yi Zhou. Last updated 5 months ago.
thirdpartyclientannotationdataimportbrendadatabaseenzymehacktoberfestcpp
2 stars 4.60 score 4 scripts
regisoc
kibior:A Simple Data Management and Sharing Tool
An interface to store, retrieve, search, join and share datasets, based on Elasticsearch (ES) API. As a decentralized, FAIR and collaborative search engine and database effort, it proposes a simple push/pull/search mechanism only based on ES, a tool which can be deployed on nearly any hardware. It is a high-level R-ES binding to ease data usage using 'elastic' package (S. Chamberlain (2020)) <https://docs.ropensci.org/elastic/>, extends joins from 'dplyr' package (H. Wickham et al. (2020)) <https://dplyr.tidyverse.org/> and integrates specific biological format importation with Bioconductor packages such as 'rtracklayer' (M. Lawrence and al. (2009) <doi:10.1093/bioinformatics/btp328>) <http://bioconductor.org/packages/rtracklayer>, 'Biostrings' (H. Pagès and al. (2020) <doi:10.18129/B9.bioc.Biostrings>) <http://bioconductor.org/packages/Biostrings>, and 'Rsamtools' (M. Morgan and al. (2020) <doi:10.18129/B9.bioc.Rsamtools>) <http://bioconductor.org/packages/Rsamtools>, but also a long list of more common ones with 'rio' (C-h. Chan and al. (2018)) <https://cran.r-project.org/package=rio>.
Maintained by Régis Ongaro-Carcy. Last updated 4 years ago.
dataimportdatarepresentationthirdpartyclientdata-sciencedatabasedatasetselasticsearchelasticsearch-clientpush-pullsearchsearch-engine
3 stars 4.48 score 8 scripts
wactbprot
R4CouchDB:A R Convenience Layer for CouchDB 2.0
Provides a collection of functions for basic database and document management operations such as add (cdbAddDoc()), get (cdbGetDoc()), list access (cdbGetList()) or delete (cdbDeleteDoc()). Every cdbFunction() gets and returns a list() containing the connection setup. Such a list (named 'cdb' in the documentation) can be generated by cdb <- cdbIni(). Moreover, cdb provides some functions respectively functionality e.g cdb$baseUrl() or cdb$getDocRev().
Maintained by Thomas Bock. Last updated 8 years ago.
31 stars 4.45 score 18 scripts
skranz
dbmisc:Tools for working with SQLite in R
Tools for working with SQLite in R, in particular support for simple YAML schemas.
Maintained by Sebastian Kranz. Last updated 2 years ago.
27 stars 4.41 score 16 scripts 4 dependents
ngiangre
kidsides:Download, Cache, and Connect to 'KidSIDES'
Caches and then connects to a 'sqlite' database containing half a million pediatric drug safety signals. The database is part of a family of resources catalogued at <https://nsides.io>. The database contains 17 tables where the description table provides a map between the fields the field's details. The database was created by Nicholas Giangreco during his PhD thesis which you can read in Giangreco (2022) <doi:10.7916/d8-5d9b-6738>. The observations are from the Food and Drug Administration's Adverse Event Reporting System. Generalized additive models estimated drug effects across child development stages for the occurrence of an adverse event when exposed to a drug compared to other drugs. Read more at the methods detailed in Giangreco (2022) <doi:10.1016/j.medj.2022.06.001>.
Maintained by Nicholas Giangreco. Last updated 2 years ago.
databasedruggeneralized-additive-modelsinformaticspediatricspharmacovigilancepkgdownsafety
5 stars 4.40 score 5 scripts
ctu-bern
redcaptools:Tools for exporting and working with REDCap data
Tools for exporting and working with REDCap data (e.g. adding labels, formatting dates).
Maintained by Alan G Haynes. Last updated 4 months ago.
4 stars 4.38 score 9 scripts
omarbenites
cropdatape:Open Data of Agricultural Production of Crops of Peru
Provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI). The first version includes 6 crops: rice, quinoa, potato, sweet potato, tomato and wheat; all of them across 24 departments. Initially, in excel files which has been transformed and assembled using tidy data principles, i.e. each variable is in a column, each observation is a row and each value is in a cell. The variables variables are sowing and harvest area per crop, yield, production and price per plot, every one year, from 2004 to 2014.
Maintained by Omar Benites-Alfaro. Last updated 6 years ago.
agricultureagroinformaticscropsdatabaseopendataperupotatoquinoaricesweettomatounalmwheat
1 stars 4.30 score 2 scripts
frbcesab
zoteror:Handle Zotero Local Database
Makes a connection to the (local) Zotero database (SQLite) to extract bibliographic references metadata.
Maintained by Nicolas Casajus. Last updated 6 months ago.
6 stars 3.95 score 5 scriptsr-dbi
dblog:Logging for DBI
Provides logging of DBI methods for arbitrary backends.
Maintained by Kirill Müller. Last updated 4 months ago.
9 stars 3.83 score 7 scriptsropensci
cRegulome:Obtain and Visualize Regulome-Gene Expression Correlations in Cancer
Builds a 'SQLite' database file of pre-calculated transcription factor/microRNA-gene correlations (co-expression) in cancer from the Cistrome Cancer Liu et al. (2011) <doi:10.1186/gb-2011-12-8-r83> and 'miRCancerdb' databases (in press). Provides custom classes and functions to query, tidy and plot the correlation data.
Maintained by Mahmoud Ahmed. Last updated 5 years ago.
cancer-genomicsdatabasedatasciencemicrornapeer-reviewedtcga-datatranscription-factors
3 stars 3.69 score 54 scripts
pr2database
pr2database:PR2 database with shiny web interface
PR2 database See https://pr2-database.org
Maintained by Daniel Vaulot. Last updated 2 years ago.
18s-rrnadatabaseeukaryotesmetabarcodingrrnataxonomy
80 stars 3.60 score 7 scripts
ropenspain
comidistar:Puntuaciones de las Catas a Ciegas de El Comidista
Base de datos documentada con las puntuaciones de las catas a ciegas de El Comidista, información sobre los productos y su precio, y metadatos sobre el vídeo subido a YouTube.
Maintained by Gonzalo Garcia-Castro. Last updated 11 months ago.
6 stars 3.48 score 4 scripts
crotman
sqliteutils:Utility Functions for 'SQLite'
A tool for working with 'SQLite' databases. 'SQLite' has some idiosyncrasies and limitations that impose some hurdles to the R developer who is using this database as a repository. For instance, 'SQLite' doesn't have a date type and 'sqliteutils' has some functions to deal with that.
Maintained by Bruno Crotman. Last updated 4 years ago.
5 stars 3.40 score 2 scriptsropensci
SymbiotaR2:Downloading Data from Symbiota2 Portals into R
Download data from Symbiota2 portals using Symbiota's API. Covers the Checklists, Collections, Crowdsource, Exsiccati, Glossary, ImageProcessor, Key, Media, Occurrence, Reference, Taxa, Traits, and UserRoles API families. Each Symbiota2 portal owner can load their own plugins (and modified code), and so this package may not cover every possible API endpoint from a given Symbiota2 instance.
Maintained by Austin Koontz. Last updated 3 years ago.
databaselibraryspecimen-recordssymbiotasymbiota2symbiota2-portal
2 stars 3.30 score 4 scripts
joelnitta
taxastand:Taxonomic Name Standardization
Matches species names to a taxonomic standard. Resolves synonyms consistently and reproducibly.
Maintained by Joel Nitta. Last updated 3 years ago.
20 stars 3.04 score 11 scripts