Observational Health Data Sciences and Informatics

Repositories

• CohortDiagnostics

  An R package for performing various cohort diagnostics.

  hades
  R 17 13 11 0 Updated May 12, 2021

• Athena

  Web application for distributing and browsing the Standardized Vocabularies for all instances of an OMOP CDM
  Java 14 33 32 4 Updated May 12, 2021

• Visualizations

  [Under development] Visualizations is a collection of JavaScript modules to support D3 visualizations in web-based applications
  JavaScript 4 7 3 1 Updated May 12, 2021

• ShinyDeploy

  Shiny apps in this repository will be automatically deployed to the OHDSI Shiny server.
  R 24 14 5 0 Updated May 12, 2021

• Achilles

  Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database
  R 84 93 6 1 Updated May 12, 2021

• DataQualityDashboard

  A tool to help improve data quality standards in observational data science.

  data-quality
  JavaScript Apache-2.0 34 44 61 6 Updated May 11, 2021

• CommonEvidenceModel

  Common Evidence Model (CEM) is a structure for standardizing evidence about drug-outcome relationship across disparate evidence sources.
  R Apache-2.0 7 12 21 0 Updated May 11, 2021

• FeatureExtraction

  An R package for generating features (covariates) for a cohort using data in the Common Data Model.

  hades
  R 46 37 20 (1 issue needs help) 2 Updated May 11, 2021

• Atlas

  ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
  JavaScript Apache-2.0 78 166 212 5 Updated May 11, 2021

• WebAPI

  OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
  Java 97 79 80 1 Updated May 11, 2021

• OncologyWG

  Oncology Working Group Repository
  Ruby Apache-2.0 13 30 98 23 Updated May 11, 2021

• PatientLevelPrediction

  An R package for performing patient level prediction in an observational database in the OMOP Common Data Model.

  hades
  R 62 110 24 1 Updated May 10, 2021

• PheValuator

  An R package for evaluating phenotype algorithms.
  R 2 7 2 0 Updated May 10, 2021

• DatabaseConnector

  An R package for connecting to databases using JDBC.

  hades
  R 46 29 14 0 Updated May 10, 2021

• WhiteRabbit

  WhiteRabbit is a small application that can be used to analyse the structure and contents of a database as preparation for designing an ETL. It comes with RabbitInAHat, an application for interactive design of an ETL to the OMOP Common Data Model with the help of the the scan report generated by White Rabbit.
  Java Apache-2.0 52 90 70 (2 issues need help) 0 Updated May 10, 2021

• AthenaUI

  UI of web application for distributing and browsing the Standardized Vocabularies for the OMOP CDM
  TypeScript 1 5 4 5 Updated May 9, 2021

• ArachneUIComponents

  [under development] a open repository to host ARACHNE Common UI components
  JavaScript Apache-2.0 1 3 0 4 Updated May 9, 2021

• GIS
  R 4 1 8 0 Updated May 7, 2021

• Vocabulary-v5.0

  PALLAS: Build process for OMOP Standardized Vocabularies. Currently not available as independent release. Therefore, do not clone or try to replicate. It is work in progress and not ready for replication.
  PLpgSQL Unlicense 48 115 119 15 Updated May 7, 2021

• SqlRender

  This is an R package and Java library for rendering parameterized SQL, and translating it to different SQL dialects.

  hades
  R 46 41 30 1 Updated May 7, 2021

• ArachneExecutionEngine

  Arachne Execution Engine is a component used to execute remote SQL or R code. It is used by both Arachne Data Node as well as WebAPI
  PLpgSQL 4 4 4 2 Updated May 6, 2021

• Tutorial-ETL

  Course materials for OHDSI ETL tutorial
  R Apache-2.0 5 16 0 0 Updated May 5, 2021

• EmpiricalCalibration

  An R package for performing empirical calibration of observational study estimates

  hades
  R 6 7 0 0 Updated May 5, 2021

• SkeletonCohortDiagnosticsStudy

  An R package that can be used as the starting point to implement a cohort diagnostics study.
  R 0 1 1 0 Updated May 4, 2021

• EvidenceSynthesis

  An R package for combining evidence from multiple sources (e.g. multiple data sites)

  hades
  R 4 3 0 0 Updated May 4, 2021

• Andromeda

  AsynchroNous Disk-based Representation of MassivE DAta: An R package aimed at replacing ff for storing large data objects.

  hades
  R 3 4 6 2 Updated May 4, 2021

• Usagi

  Usagi is an application to help create mappings between coding systems and the Vocabulary standard concepts.
  Java 17 39 19 (1 issue needs help) 0 Updated May 3, 2021

• ConceptSetDiagnostics

  Package to assist with design diagnostics for concept set
  R 2 0 1 0 Updated May 3, 2021

• Cyclops

  Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.

  hades
  C++ 23 28 7 0 Updated May 1, 2021

• CirceR

  R package wrapper for CIRCE
  R 1 3 1 0 Updated Apr 30, 2021