Observational Health Data Sciences and Informatics

Repositories

• OncologyWG

  Oncology Working Group Repository
  Ruby Apache-2.0 12 21 100 18 Updated Oct 20, 2020

• Andromeda

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

  hades
  R 3 2 4 1 Updated Oct 20, 2020

• 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 45 105 95 11 Updated Oct 20, 2020

• DatabaseConnector

  An R package for connecting to databases using JDBC.

  hades
  R 41 26 27 2 Updated Oct 20, 2020

• ArachneCentralAPI

  Arachne Central middle-tier including Service API.
  Java 3 4 3 7 Updated Oct 20, 2020

• ArachneUI

  Network infrastructure for collaborative studies across disparate data nodes and researches
  SCSS 3 13 3 5 Updated Oct 20, 2020

• ArachneNodeAPI

  Arachne Data Node is a component that facilitates connection and communication between local databases and Arachne Central
  Java 0 2 5 5 Updated Oct 20, 2020

• Achilles

  Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database
  R 80 82 85 4 Updated Oct 20, 2020

• TheBookOfOhdsi

  The Book of OHDSI repository
  R CC0-1.0 46 49 14 4 Updated Oct 19, 2020

• Atlas

  ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
  JavaScript Apache-2.0 71 141 200 9 Updated Oct 19, 2020

• WebAPI

  OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
  Java 90 69 73 6 Updated Oct 19, 2020

• DataQualityDashboard

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

  data-quality
  JavaScript Apache-2.0 30 33 71 7 Updated Oct 19, 2020

• CohortDiagnostics

  An R package for performing various cohort diagnostics.

  hades
  R 12 7 34 0 Updated Oct 19, 2020

• Cyclops

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

  hades
  C++ 21 26 6 0 Updated Oct 19, 2020

• ShinyDeploy

  Shiny apps in this repository will be automatically deployed to the OHDSI Shiny server.
  R 15 6 4 0 Updated Oct 18, 2020

• PhenotypeLibrary

  A repository to store, organize and maintain the content of the OHDSI Phenotype library.
  R Apache-2.0 8 10 0 0 Updated Oct 17, 2020

• CommonDataModel

  Definition and DDLs for the OMOP Common Data Model (CDM)
  Batchfile Apache-2.0 293 488 130 15 Updated Oct 16, 2020

• CdmDdlBase

  An R package for generating the documentation and DDL (Data Definition Language) for the Common Data Model in various SQL dialects
  HTML Apache-2.0 1 0 3 0 Updated Oct 16, 2020

• Eunomia

  A standard CDM dataset for testing and demonstration purposes.

  hades
  R 5 5 3 0 Updated Oct 16, 2020

• Hades

  Health Analytics Data-to-Evidence Suite (HADES): A collection of R packages for performing analytics against the Common Data Model.

  hades
  R Apache-2.0 1 1 1 0 Updated Oct 16, 2020

• Broadsea-Shiny

  A Docker container based on rocker/shiny with added java jdk and additional R packages.
  Dockerfile MIT 2 2 0 0 Updated Oct 15, 2020

• SkeletonExistingPredictionModelStudy

  A skeleton package to use as a template for studies validating existing prediction models

  skeleton patient-level-prediction
  R 1 2 1 0 Updated Oct 15, 2020

• circe-be

  CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5

  cohort-definitions
  Java Apache-2.0 6 4 8 4 Updated Oct 15, 2020

• PatientLevelPrediction

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

  hades
  R 52 90 27 2 Updated Oct 15, 2020

• ParallelLogger

  An R package for easy parallel computing, logging, and function call automation.

  hades
  R 3 6 1 0 Updated Oct 15, 2020

• OHDSI-in-a-Box

  Virtual Machine containing SynPUF data in OMOP CDM, a RDBS including query client, WebAPI, ATLAS, R and Python.
  Apache-2.0 12 17 1 0 Updated Oct 14, 2020

• ArachneCommons

  Commons module contains common code re-used between all Arachne components
  Java 3 2 2 1 Updated Oct 14, 2020

• Authenticator

  [in development] A shared component to allow user authenication across OHDSI web-based applications
  Java Apache-2.0 1 1 1 1 Updated Oct 13, 2020

• RiskStratifiedEstimation

  [Under development] An R package for performing effect estimation in risk strata derived from predictive models.
  R 2 0 0 0 Updated Oct 13, 2020

• StandardizedAnalysisAPI

  Interfaces for standardized OHDSI analyses (Cohort Characterization, TxPathway, Incidence Rate etc.) used as an exchange standard or implementation guide
  Java Apache-2.0 3 2 1 6 Updated Oct 13, 2020