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    10
  • Rank 1,807,489 (Top 36 %)
  • Language
    R
  • License
    Apache License 2.0
  • Created about 8 years ago
  • Updated about 1 month ago

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Repository Details

More Repositories

1

CommonDataModel

Definition and DDLs for the OMOP Common Data Model (CDM)
HTML
883
star
2

Atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data
JavaScript
266
star
3

Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
PLpgSQL
214
star
4

PatientLevelPrediction

An R package for performing patient level prediction in an observational database in the OMOP Common Data Model.
HTML
187
star
5

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
177
star
6

DataQualityDashboard

A tool to help improve data quality standards in observational data science.
JavaScript
136
star
7

WebAPI

OHDSI WebAPI contains all OHDSI services that can be called from OHDSI applications
Java
128
star
8

Achilles

Automated Characterization of Health Information at Large-scale Longitudinal Evidence Systems (ACHILLES) - descriptive statistics about a OMOP CDM database
R
128
star
9

TheBookOfOhdsi

The Book of OHDSI repository
R
104
star
10

ETL-Synthea

A package supporting the conversion from Synthea CSV to OMOP CDM
R
97
star
11

Usagi

Usagi is an application to help create mappings between coding systems and the Vocabulary standard concepts.
Java
91
star
12

ETL-CMS

Workproducts to ETL CMS datasets into OMOP Common Data Model
Python
84
star
13

CohortMethod

An R package for performing new-user cohort studies in an observational database in the OMOP Common Data Model.
R
82
star
14

SqlRender

This is an R package and Java library for rendering parameterized SQL, and translating it to different SQL dialects.
R
77
star
15

OHDSIonAWS

Automation code and documentation for standing up the OHDSI toolstack in an AWS environment
Shell
72
star
16

Broadsea

Broadsea deploys the core OHDSI technology stack (Atlas & R Hades), using cross-platform Docker container technology.
R
70
star
17

MIMIC

MIMIC (Medical Information Mart for Intensive Care) is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. This repository contains the ETL to the OMOP CDM.
Python
70
star
18

Athena

Web application for distributing and browsing the Standardized Vocabularies for all instances of an OMOP CDM
Java
57
star
19

FeatureExtraction

An R package for generating features (covariates) for a cohort using data in the Common Data Model.
R
57
star
20

OncologyWG

Oncology Working Group Repository
Ruby
56
star
21

KnowledgeBase

Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and health outcomes of interest.
HTML
55
star
22

DatabaseConnector

An R package for connecting to databases using JDBC.
R
54
star
23

Criteria2Query

[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDM
Java
49
star
24

ETL-CDMBuilder

ETL-CDMBuilder is a repo containing a .NET Core application to perform ETL to OMOP CDM for multiple databases
C#
49
star
25

OHDSI-in-a-Box

Virtual Machine containing SynPUF data in OMOP CDM, a RDBS including query client, WebAPI, ATLAS, R and Python.
49
star
26

Tutorial-ETL

Course materials for OHDSI ETL tutorial
R
45
star
27

Eunomia

An R package that facilitates access to a variety of OMOP CDM sample data sets.
R
42
star
28

CohortDiagnostics

An R package for performing various cohort diagnostics.
R
41
star
29

PhenotypeLibrary

A repository to store, organize and maintain the content of the OHDSI Phenotype library. OHDSI Forum post https://forums.ohdsi.org/t/ohdsi-phenotype-library-announcements/16910
R
38
star
30

StudyProtocols

Repository of OHDSI Collaborative Research Protocols
R
37
star
31

Cyclops

Cyclops (Cyclic coordinate descent for logistic, Poisson and survival analysis) is an R package for performing large scale regularized regressions.
C++
34
star
32

Aphrodite

[in development]
R
33
star
33

NLPTools

[in development] Tools to support Natural Language Processing of freetext to create structured data elements for analysis
Java
32
star
34

StudyProtocolSandbox

This repository is for developing study packages for OHDSI studies. Once completed, they can be moved to the StudyProtocols repository.
R
32
star
35

Perseus

[under development] Tools for ETL into OMOP CDM and deployment of OHDSI toolstack
TypeScript
32
star
36

Themis

Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
27
star
37

ShinyDeploy

Shiny apps in this repository will be automatically deployed to the OHDSI Shiny server.
R
26
star
38

OMOP-Queries

Jupyter Notebook
23
star
39

Hades

Health Analytics Data-to-Evidence Suite (HADES): A collection of R packages for performing analytics against the Common Data Model.
R
23
star
40

Tutorial-CDM

Training materials for Vocabulary & CDM Tutorial.
TSQL
20
star
41

ClinicalTrialsWGETL

[under development] ETL materials to support proposal for CDM enhancements for clinical trial data
HTML
20
star
42

AchillesWeb

Interactive web site for reviewing the results of the Achilles R package.
JavaScript
19
star
43

bayes-bridge

Bayesian sparse regression with regularized shrinkage and conjugate gradient acceleration
Jupyter Notebook
19
star
44

Genomic-CDM

Repository for development of the genomic module of the CDM.
18
star
45

PheValuator

An R package for evaluating phenotype algorithms.
R
17
star
46

Radiology-CDM

Pilot model and converter for integration of radiology data into OMOP-CDM
R
17
star
47

FhirToCdm

Conversion from FHIR HL7 to OMOP CDM
C#
16
star
48

FuzzyForest

[Under development] Random classification and regression trees
R
16
star
49

Capr

Cohort definition Application Programming in R
R
15
star
50

dbt-synthea

[Under development] A dbt ETL project to convert a Synthea synthetic data set into the OMOP CDM
Python
15
star
51

CommonEvidenceModel

Common Evidence Model (CEM) is a structure for standardizing evidence about drug-outcome relationship across disparate evidence sources.
R
14
star
52

InspectOMOP

InspectOmop is a lightweight python 3 package that assists in the extraction of electronic health record(EHR) data from relational databases following the OHDSI OMOP Common Data Model(CDM) standard v>=5.
Python
14
star
53

ArachneUI

Network infrastructure for collaborative studies across disparate data nodes and researches
SCSS
14
star
54

ETL-LambdaBuilder

CDM Builder leveraging AWS Lambda
C#
14
star
55

CureIdRegistry

TSQL
14
star
56

SelfControlledCaseSeries

An R package for performing Self-Controlled Case Series (SCCS) analyses in an observational database in the OMOP Common Data Model.
R
13
star
57

QueryLibrary

This is an R package that implements a library of standard queries that run against the OMOP-CDM.
R
13
star
58

Covid-19

The OHDSI repository to provide comprehensive evidence for the covid-19
HTML
13
star
59

OMOP-Standardized-Vocabularies

This repository is not longer active. It used to have the only purpose of creating releases of the Standardized Vocabularies, i.e. the content, not those of the Pallas Vocabulary Build System itself. As of 17-July-2018, vocabulary releases are also processed by Pallas. Please visit https://github.com/OHDSI/Vocabulary-v5.0/releases.
13
star
60

RcppXsimd

R package wrapper for the C++ header-only library Xsimd that provides parallelized math implementations using SIMD
C++
12
star
61

Ares

A Research Exploration System
Vue
12
star
62

CohortGenerator

Cohort Generation for the OMOP Common Data Model
R
11
star
63

Andromeda

AsynchroNous Disk-based Representation of MassivE DAta: An R package aimed at replacing ff for storing large data objects.
R
11
star
64

Apollo

[Under development] Assessment of Pre-trained Observational Large Language-models in OHDSI (APOLLO)
Python
11
star
65

DeepPatientLevelPrediction

An R package for performing patient level prediction using deep learning in an observational database in the OMOP Common Data Model.
R
11
star
66

ROhdsiWebApi

An R package for interfacing with a WebAPI instance
R
10
star
67

EmpiricalCalibration

An R package for performing empirical calibration of observational study estimates
R
10
star
68

ParallelLogger

An R package for easy parallel computing, logging, and function call automation.
R
10
star
69

Broadsea-WebTools

A Docker container that includes the OHDSI WebAPI (running in Apache Tomcat) and the OHDSI web applications.
Dockerfile
10
star
70

circe-be

CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5
Java
9
star
71

Koios

Tool to identify concept in the OMOP Genomic vocabulary from VCF and other files as well as HGVS notations
R
9
star
72

Visualizations

[Under development] Visualizations is a collection of JavaScript modules to support D3 visualizations in web-based applications
JavaScript
8
star
73

ETL-German-FHIR-Core

ETL process from FHIR (defined by the German Medical Informatics Initiative) to OMOP
Java
8
star
74

Tutorial-PLP

R
8
star
75

OMOPV4_PCORNetV1_ETL

ETL script to transform data from OMOP v4 CDM to PCORNet V1 CDM
8
star
76

CaseControl

An R package for performing (nested) matched case-control analyses in an observational database in the OMOP Common Data Model.
R
8
star
77

EvidenceSynthesis

An R package for combining evidence from multiple sources (e.g. multiple data sites)
R
8
star
78

OhdsiShinyModules

An R package containing Shiny modules used by various OHDSI Shiny apps
R
8
star
79

Nostos

Navigate OMOP-structured data via text-to-SQL
Jupyter Notebook
7
star
80

ETL---Korean-NSC

ETL code for converting Korean National Sample Cohort (NSC) derived from national insurance health service into OMOP-CDM v5 developed by Ajou University
R
7
star
81

ImageWG

Repository for medical image working group
Rich Text Format
7
star
82

OSIM-v5

An updated version of OSIM for CDM v5
PLpgSQL
7
star
83

Strategus

[Under development] An R packages for coordinating and executing analytics using HADES modules
R
7
star
84

AthenaUI

UI of web application for distributing and browsing the Standardized Vocabularies for the OMOP CDM
TypeScript
6
star
85

BigKnn

An R package implementing a large scale k-nearest neighbor classifier using the Lucene search engine
R
6
star
86

IcTemporalPatternDiscovery

An R package for performing the IC Temporal Pattern Discovery method.
R
6
star
87

Legend

An R package implementing Large-Scale Evidence Generation and Evaluation in a Network of Databases (LEGEND).
R
6
star
88

OhdsiRTools

An R package of support tools that didnโ€™t fit other categories, including tools for maintaining R libraries.
R
6
star
89

DbDiagnostics

Package to profile a database and execute data diagnostics based on individual analysis settings
R
6
star
90

CohortIncidence

Contains the Java and R assets to perform Incidence calculations on a CDM
R
6
star
91

CirceR

R package wrapper for CIRCE
R
6
star
92

SelfControlledCohort

An R package for performing self-controlled cohort analyses, a method to estimate risk by comparing time exposed with time unexposed among the exposed cohort.
R
6
star
93

MethodEvaluation

An R package for the evaluation of estimation methods
R
6
star
94

Hermes

(DEPRECATED) HERMES is a vocabulary browser tool for OMOP CDM v5
JavaScript
6
star
95

Hestia

Hestia is an API for function calling on the OMOP CDM.
Python
6
star
96

Circe

[Under development] CIRCE is a cohort definition and syntax compiler tool for OMOP CDMv5
JavaScript
5
star
97

EunomiaDatasets

Hosting of sample CDM datasets in CSV format for use in testing throughout the OHDSI community. Eunomia R package to manage the datasets can be accessed at https://github.com/OHDSI/Eunomia.
5
star
98

ArachneCentralAPI

Arachne Central middle-tier including Service API.
Java
5
star
99

Calypso

CALYPSO (Criteria Assessment Logic for Your Population Study in Observational data) is a web user interface to define, instantiate and evaluate a study population and the implications of inclusion criteria
JavaScript
5
star
100

StandardizedAnalysisAPI

Interfaces for standardized OHDSI analyses (Cohort Characterization, TxPathway, Incidence Rate etc.) used as an exchange standard or implementation guide
Java
5
star