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CohortExplorer is part of HADES.


This software tool is designed to extract data from a randomized subset of individuals within a cohort and make it available for exploration in a ‘Shiny’ application environment. It retrieves date-stamped, event-level records from one or more data sources that represent patient data in the Observational Medical Outcomes Partnership (OMOP) data model format. This tool features a user-friendly interface that enables users to efficiently explore the extracted profiles, thereby facilitating applications, such as reviewing structured profiles. The output of this R-package is a self-contained R shiny that contains person-level data for review.


  • Contains person level data. This package is not to be considered de-identified.
  • Please do not share the output with others as it may violate protected health information.
  • .RDS file in output contains PHI.


  • From an instantiated cohort, identifies specified number of random persons. It also allows for non random selection by specifying a set of personId as input.
  • Extracts person level data for each person from the common data model, and constructs a results object in rds form. This rds object has person level data with personId and dates.
  • Allows additional de-identification using two optional mechanisms (shift dates and replace OMOP personId with a new random id). Shift date: shifts all dates so that the first observation_period_start_date for a person is set to January 1st 2000, and all other dates are shifted in relation to this date. Also creates and replaces the source personId with a new randomly generated id.
  • Creates a R shiny app in a specified local folder, that can then be published to a shiny server or explored locally.
  • Allows navigation of patient event data using configurable parameters from within the shiny application, e.g. regular expression to filter event.


CohortExplorer shiny app screenshot
CohortExplorer shiny app screenshot

How to use

  • The output of createCohortExplorerApp is a shiny App with person level data in .rds. It is in the output folder.
  • Go the output location in your file browser (e.g. windows file explorer in a Windows computer) and start ‘CohortExplorer.Rproj’.
  • Optionally, in R console now run renv::restore() to enable renv. This will download all required packages and dependencies and set up the run environment.
  • Next call to shiny::runApp()
  • If you want to run this shiny App on a remote Shiny Server, you may copy all the files in the output to the remote shiny servers new app file folder. run renv::restore() in the shiny server and restart app.


CohortExplorer is an R package.

System Requirements

Requires R (version 4.0.0 or higher).


  1. See the instructions here for configuring your R environment, including RTools and Java.

  2. In R, use the following commands to download and install CohortExplorer:


User Documentation

Documentation can be found on the package website.

PDF versions of the documentation are also available: * Package manual: CohortExplorer.pdf



Read here how you can contribute to this package.


CohortExplorer is licensed under Apache License 2.0


CohortExplorer is being developed in R Studio.

Development status

CohortExplorer is under development.