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opalr - 'Opal' Data Repository Client and 'DataSHIELD' Utils

Data integration Web application for biobanks by 'OBiBa'. 'Opal' is the core database application for biobanks. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is typically used in a research center to analyze the data acquired at assessment centres. Its ultimate purpose is to achieve seamless data-sharing among biobanks. This 'Opal' client allows to interact with 'Opal' web services and to perform operations on the R server side. 'DataSHIELD' administration tools are also provided.

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8.72 score 3 stars 3 dependents 201 scripts 911 downloads

DSI - 'DataSHIELD' Interface

'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package defines the API that is to be implemented by 'DataSHIELD' compliant data repositories.

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7.18 score 2 stars 7 dependents 242 scripts 806 downloads

resourcer - Resource Resolver

A resource represents some data or a computation unit. It is described by a URL and credentials. This package proposes a Resource model with "resolver" and "client" classes to facilitate the access and the usage of the resources.

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6.19 score 3 stars 2 dependents 43 scripts 728 downloads

DSLite - 'DataSHIELD' Implementation on Local Datasets

'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This 'DataSHIELD Interface' implementation is for analyzing datasets living in the current R session. The purpose of this is primarily for lightweight 'DataSHIELD' analysis package development.

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5.38 score 4 stars 119 scripts 661 downloads

DSOpal - 'DataSHIELD' Implementation for 'Opal'

'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This package is the 'DataSHIELD' interface implementation for 'Opal', which is the data integration application for biobanks by 'OBiBa'. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. 'Opal' is such a central repository. It can import, process, validate, query, analyze, report, and export data. 'Opal' is the reference implementation of the 'DataSHIELD' infrastructure.

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4.57 score 245 scripts 603 downloads

micar - 'Mica' Data Web Portal Client

'Mica' is a server application used to create data web portals for large-scale epidemiological studies or multiple-study consortia. 'Mica' helps studies to provide scientifically robust data visibility and web presence without significant information technology effort. 'Mica' provides a structured description of consortia, studies, annotated and searchable data dictionaries, and data access request management. This 'Mica' client allows to perform data extraction for reporting purposes.

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4.52 score 33 scripts 284 downloads

odbc.resourcer - Open Database Connectivity Resource Resolver

A database resource that is accessible through the Open Database Connectivity ('ODBC') API. This package uses the Resource model, with URL "resolver" and "client", to dynamically discover and make accessible tables stored in a 'MS SQL Server' database. For more details see Marcon (2021) <doi:10.1371/journal.pcbi.1008880>.

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4.48 score 3 scripts 218 downloads

rechaRge - HydroBudget – Groundwater Recharge Model

HydroBudget is a spatially distributed groundwater recharge model that computes a superficial water budget on grid cells with outputs aggregated into monthly time steps. It was developed as an accessible and computationally affordable model to simulate groundwater recharge over large areas (thousands of km2, regional-scale watersheds) and for long time periods (decades), in cold and humid climates. Model algorithms are based on the research of Dubois, E. et al. (2021a) <doi:10.5683/SP3/EUDV3H> and Dubois, E. et al. (2021b) <doi:10.5194/hess-25-6567-2021>.

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3.54 score 7 stars 5 scripts 205 downloads

s3.resourcer - S3 Resource Resolver

A S3 resource is provided by Amazon Web Services S3 or a S3-compatible object store (such as Minio). The resource can be a tidy file to be downloaded from the object store, or a data lake (such as Delta Lake) Parquet file to be read by Apache Spark.

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2.70 score 3 scripts 228 downloads

rockr - 'Rock' R Server Client

Connector to the REST API of a 'Rock' R server, to perform operations on a remote R server session, or administration tasks. See 'Rock' documentation at <https://rockdoc.obiba.org/>.

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1.74 score 11 scripts 222 downloads