special readme repo

Python

Python

R

JavaScript

A lightweight visualization for genetic sequence alignments

Groovy

API Standards for 18F

Python

Protein analysis pipeline for characterizing influenza antigenic drift

Nextflow

Ruby

An application to assist Utah CDC's Newborn Screening Program

Jupyter Notebook

A fast, lightweight implementation of Smith-Waterman

Java

CDC collaboration on blockchain prototypes.

Proof of project for CDC's r&d with using blockchain to support TB

Python

The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples

Nextflow

Culture-Independent Whole Genome Sequencing (CIWGS) Read Filter Pipeline 🧪🧬🖥️

HTML

A Simple Demonstration of Organizing Bubbles using D3v5

Java

The Cancer Report Validator (CRV) is an interactive tool for validating the content of electronic submissions of cancer-related medical information prior to a system's communication with a public health central cancer registry.

JavaScript

JavaScript

React component for visualizing your data on a map of the United States based off work done for the CDC

TypeScript

CDC OpenViz is a library of React packages for data visualization.

TypeScript

HTML

Portal site for all CDCgov projects, https://cdcgov.github.io

Java

The purpose of this project is to deliver tools that support production and consumption of HL7 and flat file formats used to communicate COVID-19 vaccination data between IIS and CDC to support tracking of vaccination progress for COVID-19.

CSS

CDC Data Hub Lifecycle, Analysis & Visualization Accelerator (LAVA) REACT Components based on machine readable requirements.

Python

GitHub Actions by CDC's CFA team

Python

Python

Python

Modeling pipeline config validation microservice.

R

R

R package for real-time Rt estimation with penalized splines

Python

Python

R

Python

Dockerfile

Widget: Test-negative study design for estimating vaccine efficacy

R

Modeling of M. genitalium and Chlamydia trachomatis, CFA-UW Collaboration

Python

R

Basic functionality for interacting with Azure from R

Python

Python

Childhood immunization demand calculator

Python

Rust

A rust crate that automatically cleans up a gene alignment by trimming to ORF and identifying and/or removing problematic sequences.

18F's code of conduct.

Go

Shell

PaaS & Containers CoP Application Demo Libarary

Shell

R

Estimating the generation time for COVID-19 transmission using household data in the United States, December 2021 – May 2023

R

R

A repository run by the US CDC to collect forecasts of weekly incident COVID-19 hospital admissions.

Jupyter Notebook

Projections of COVID-19, in standardized format

[Retiring Oct 7th, 2022] This project collects automated screening protocols and self-checker algorithms from organizations implementing CDC screening protocols in interactive web sites, chat bots, and other technology.

R

R

Privacy review and statistical disclosure control methods for covid public case data.

Perl

C#

SDK for working with case notification messages and message mapping guides

HTML

A little web tool to help people translate CSVs to FASTA and vice-versa.

Example demo of terraform functionality

Shell

Python

Dash Demonstration of the File Uploader and Dynamic Populating Dropdown Menu

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

JavaScript

This repository is for public documentation and examples for the CDC Enterprise Data Exchange (EDE/DEX) API

Go

For Data Exchange in csv format

Contains Databricks notebooks to facilitate data observability dashboards for the CDC data-exchange (DEX).

Go

C#

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

JavaScript

Kotlin

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Python

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

TypeScript

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Kotlin

The Public Health Data Observability (PHDO) Processing Status API (PS API) was developed to provide visibility into the status and performance of file uploads. The PS API provides the ability to receive reports about the status of uploads, and to develop custom queries to ask detailed questions about the data being uploaded and processed.

Kotlin

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Go

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Kotlin

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Enterprise Data Exchange (DEX) is a new cloud-native centralized data ingestion, validation, and observation service scoped for common data types (HL7, FHIR, CDA, XML, CSV) sent to the CDC. It helps public health stakeholders who send data to the CDC while reducing the maintenance efforts, complexity, and duplication of ingestion points to CDC.

Perl

Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)

HTML

HCL

HCL

HCL

HTML

TypeScript

A FHIR client allowing public health agencies to query health care organizations directly or via a TEFCA QHIN

JavaScript

Dockerfile

This is the repository for the CDCgov Maven Docker image tags

Python

CDC/CFA/Predict/Scenarios ODE Modeling Framework

Java

Perl

A collection of scripts for editing and manipulating multiple sequence alignment files.

SAS

JavaScript

SMART on FHIR app to integrate environmental health data

SAS

JavaScript

Easily generate API call statements for accessing data from ephtracking.cdc.gov

JavaScript

Environmental Public Health Visualizations

JavaScript

Assistant that helps you to create environmental health visualizations that easily can be embedded in your website

R

R interface to the CDC National Public Health Tracking Network API

Estimate epidemiological delay distributions for infectious diseases

TypeScript

JavaScript

Example UI for a Datalake Dashboard

JavaScript

Example UI for an HL7 Combiner Tool

R

Deliverables and Status reports from CS 6440 Introduction to Health Informatics

This is a central repository with high level information on Foundation Services, tutorials, example code, etc.

Java

This is the repository with the Java SDK for Foundation Services.

JavaScript

This is the repository with the JavaScript SDK for Foundation Services.

Java

This is the repository with the Java Library for Foundation Services Kafka workers.

FreeMarker

This is the repository with the CDA utilities service to parse, validate and generate sample CDA data.

Java

This is the repository with the Combiner service to combine JSON files into a single CSV or XLSX file.

This is the repository for the cryptography microservice.

HTML

This is the repository with the API gateway to connect the other microservices together.

Java

This is the repository with the HL7 utilities service to parse, validate and generate sample HL7 data.

Java

This is the repository with the Indexing layer for the Data Lake. This is the navigation layer.

Java

This is the repository with the Microsoft Utilities microservice for parsing Microsoft formatted documents.

Java

This is the repository with the Object layer for the Data Lake. This is the mutable layer.

Java

This is the repository for the reporting microservice.

Java

This is the repository that contains the Kafka workers to handle the generation of reports.

Java

This is the repository with the Business Rules Engine for ingesting and validating JSON files.

Java

This is the repository with the Storage layer for the Data Lake. This is the immutable layer.

JavaScript

A stubbing service for testing against the various endpoints of the FDNS Microservices without running the full microservices in the background.

Java

This the repository with the Java Library for the Business Rules Engine.

HTML

Testing GitHub Pages for FDNS-UI

JavaScript

A collection of reusable React components for quickly building modern and accessible web applications.

JavaScript

This project includes documentation and examples for the FDNS React UI Library.

Rust

Experimental HL7 FHIR Validator.

JavaScript

A little library to work with Javascript File objects

Repository for CDC's Flu Division

R

R

Shell

R

R

R tools for short-term forecasting

Python

A Python package for common pre- and post-processing operations done by CFA Predict for short term forecasting, nowcasting, and scenario modeling.

XSLT

GaTech-Fall2017-Davis-dohMPI-SPYNdoctors

JavaScript

GaTech-Fall2017-Duncan-BirthCerts-iHealth

JavaScript

GaTech-Fall2017-Goodman-HealthWeight-TeamScienceFreaks

C#

GaTech-Fall2017-Krupa-Concussion-FHIRStarters

Ruby

GaTech-Fall2017-Newborn-FHIRFighters

JavaScript

GaTech-Fall2017-Srinivasan-ImproveAdherence-DEVSonFHIR

JavaScript

GaTech-Fall2017-Srinivasan-SocialDeterminant - GT-MKSM

Java

GaTech-Fall2017-Srinivasan-Stroke-Team1

JavaScript

GaTech-Fall2017-Wilmore-Breastfeeding-WeDidntStartTheFHIR

Python

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

GeneFlow Public Reference Workflows

Python

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

R

Manage sets of parameters with the "griddle" format

This is the repository for the projects from the 2018 Open CDC Hackathon

HTML

Standalone Hantavirus visualization engine, powered by MicrobeTrace

Python

HIE Automation testing framework - OpenMRS, OpenHIM, OpenSHR, HAPI-FHIR, OpenEMPI

R

Python

Kotlin

Scala

Library to help with HL7 parsing, validation, transformation

Java

Converts HL7 v2 Messages to FHIR Resources

Kotlin

Python

SAS to CSV microservice

Perl

R

Import survey: Import data into R, with an application to the National Center for Health Statistics (NCHS)

R

Generation of figure by routine reporting for the case surveillance section used for IM slide 1 during summer of 2020 for COVID19 response

R

Estimating the generation time for influenza transmission using household data in the United States

R

A code-only repo of the ITF Dashboard backend

R

Contains functions for pulling publicly-available global COVID-19 case and testing data for analysis and populating a Power BI dashboard. ARCHIVED: See ITF-Dashboard Repository for further development

Rust

Rust

Shell

Dockerfile

Jenkins worker container image for performing a sonarqube CLI scan

C

Command-line JSON processor

Shell

Kmer Pathogen Identification Platform

Shell

This repository contains bioinformatics scripts and a Docker container to perform the in silico prediction of Legionella pneumophila serogroup from short read sequences using a supervised machine learning approach.

Perl

Shell

Java

Go

Kotlin

The lib-hl7v2-bumblebee library takes an HL7 v2.x message and transforms it into a JSON tree.

Kotlin

The lib-hl7v2-nist-validator is a wrapper around the NIST HL7v2 Validator.

Shell

Python

LpSubP is a rapid subtyping tool for Legionella pneumophila with core gene set

R

This repository provides tool templates for malaria focused health facility surveys.

Jupyter Notebook

See Readme

This repository is a collection of artifacts with the gov.cdc group id for use in Java projects through the Maven build tool.

R

Real-Time Use of a Dynamic Model to Measure the Impact of Public Health Interventions on Measles Outbreak Size and Duration — Chicago, Illinois, 2024", MMWR (2024)

HTML

A Portfolio Website for the Molecular Epi and Bx Team

TSQL

TypeScript

The Visualization Multitool for Molecular Epidemiology and Bioinformatics

HTML

Sequence analysis and data visualization tool

TypeScript

R

A little R package to Launch MicrobeTrace in a Shiny Server

Python

Nextflow

R

Shell

Shell

This workflow prepares and aligns samples using BWA for variant calling using the MycoSNP GATK workflow.

This workflow prepares a reference index using BWA as part of the MycoSNP suite of workflows.

This workflow calls variants for MycoSNP using GATK.

Nextflow

CDCgov/mycosnp-nf

SAS

Code for analyzing vital statistics mortality data, including death certificate literal text

R

Python

Identify bursts of HIV transmission across a clock-tree

HTML

This repository contains an analysis pipeline developed to characterize WGS output

JavaScript

R

NCHS data: public use files (PUFs) from the National Center for Health Statistics (NCHS)

CDC Vaccine Safety Datalink COVID-19 Vaccination Coverage Among Persons 16 years and Older, Dec 2020-May 2021

TypeScript

Java

Python

Java

Java

Data Ingestion for Modernization of NEDSS Project by Enquizit

Java

Python

Sandbox to test concepts and experiments without impacting the NEDSS-DataIngestion

TSQL

Data Near Real Time Reporting micro services for Modernized NBS System

Java

Smarty

This repository is created for NEDSS Helm charts.

HCL

Java

Java

Dockerfile

JavaScript

Use Neighbor-Joining to turn distance matrices into phylogenetic trees in Browser and Node.js

Jupyter Notebook

NeST NextFlow

HTML

Python

Python API to NIS data

HTML

Natural Language processing for Pathology reports on cancer histology, laterality, side, and behavior.

R

An R package that provides nearest-neighbors matching and analysis of case-control data.

R

Data repository for NWSS

Python

Dockerfile

Version of the SonarQube container image that will run in the OpenShift restricted SCC.

JavaScript

A client-side webapp to scrape data from the standard Epidemiological Interview Record

Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.

Nextflow

ONT-Seq-analysis is a specialized pipeline designed for analyzing Oxford Nanopore Technologies (ONT) sequencing data from Mpox isolates. It performs reference-based assemblies, identifies variants, designates clades, and generates a detailed quality control (QC) report.

HTML

This is the repository for the openCDC web site. Entire site is generated from data files describing CDC Open Technology types for data, api, code, and events. All CDC programs are welcome to submit pull requests with updates and new items useful to the public health open source community.

Shell

Python

Code to search clinical notes text for opioid involvement

Python

Code to flag ICD-10-CM codes related to opioid involvement, substance use disorder, and mental health issues in structured hospital data

Jupyter Notebook

Polio and Picornavirus Laboratory Branch (PPLB)

Shell

HTML

A Phylogenetics toolkit for Javascript

HTML

Jupyter Notebook

Python

Terraform and Python code for deploying PHDI pipelines to Google Cloud Platform.

HCL

Jupyter Notebook

PHIN VADS Lite data

Go

A complete rewrite of CDC's vocabulary management service, PHIN VADS, in Go.

Ruby

JavaScript

C#

JavaScript

Python

🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens

HTML

A Radical Alternative to Conventional Phylogenetic Tree Renderers

Kotlin

Project for HL7 Dev Days 2019 Redmond. Converts V2 PIDs to FHIR Patient Resources

HTML

A simple, all-client-side web app to transform Adjacency lists into Edge Lists

Python

R

Functions for statistical estimation with pooled or grouped binary data

PoSE: (Pattern of Sequence Evolution) provides visualization and annotation of amino acid substitutions to help determine major patterns during sequence evolution of protein-coding sequences, hypervariable regions, or changes in dN/dS ratios.

HTML

R

Python

JavaScript

JavaScript

Kotlin

The CDC’s Pandemic-Ready Interoperability Modernization Effort (PRIME) Java based FHIR conversion library

Rich Text Format

Kotlin

HCL

Repository for the joint CDC+USDS PRIME project's Data Ingestion prototype project. The goal is to work with raw vaccine, case, and lab report data to arrive at an analysis of breakthrough cases in the state of Virginia that uses a data lake as underlying storage.

Kotlin

ReportStream is a public intermediary tool for delivery of data between different parts of the healthcare ecosystem.

Java

SimpleReport is a fast, free, and easy way for COVID-19 testing facilities to report results to public health departments.

JavaScript

Landing / marketing site for the SimpleReport application

JavaScript

Pick a county, see its neighbors

Python

Python

Python

A Python package for the National Syndromic Surveillance Program (NSSP) and its Community of Practice. A collection of classes and methods to advance the practice of Syndromic Surveillance.

Python

Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro.

Python

A replication in Python and PyRenew of a renewal model written in Epidemia for forecasting influenza hospital admissions.

Python

Models and infrastructure for forecasting COVID-19 and Flu hospitalizations using wastewater data with PyRenew

JavaScript

Starter kit for use in creating new React projects

Python

The RecordLinker is a service that links records from two datasets based on a set of common attributes. The service is designed to be used in a variety of public health contexts, such as linking patient records from different sources or linking records from different public health surveillance systems.

Go

TypeScript

Intelligent Data Workflow Automation

Python

R

A Signature R package for the National Syndromic Surveillance Program (NSSP) at the Centers for Disease Control and Prevention (CDC). A collection of tools, classes and functions that supports the Community of Practice of the NSSP.

R

Rnssp R Markdown templates are custom-built, parameterized R Markdown templates with seamless integration to the Rnssp R package to enhance user experiences and streamline workflows.

R

Rnssp Shiny Apps are custom-built applications with seamless integration to the Rnssp R package.

HTML

Online Documentation for Rnssp R Markdown Templates

Build the Rnssp R package for webr and shinylive.

R

Rate Stabilizing Tool R Package: Gibbs Samplers for Bayesian Spatiotemporal CAR Models

Julia

Shell

Ruby Source-to-Image builder tailored to the needs of the SDP Vocabulary project.

Python

Remove host contaminants from sequencing files

Python

Remove Host Reads from Paired End Sequencing

R

Jupyter Notebook

Jupyter Notebook file with R Script for FRNT50 Calculations from a folder of CSV files in 96-well plate format.

R

Perl

A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.

R

MPX Helper Functions for the Situational Awareness and Visualization Team

R

The purpose of SaviR is to collect the functions needed to access and prepare various COVID data sources.

Scala

Nextflow

An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as a base

Python

Python

Python library for getting metadata from source code hosting tools

Jinja

Repository for CDC's Surveillance Data Platform project.

Java

HTML

Smarty

Customized Jenkins Docker image for OpenShift using OCP Jenkins S2I builder

R

Demonstrations of deploying machine learning models in R, MLflow, and ECPaaS

Repository for the SDP team to test slides.

JavaScript

Repository for the SDP Vocabulary Service.

Java

GUI for calculating TN93 or SNP distances for a set of sequences.

HTML

Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories

R

Spawn Normally-Distributed Mutant DNA Sequences

Jupyter Notebook

R

Run Shiny. Make Gantt Charts.

R

R

R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net

C#

An application and Wiki for managing an inventory of source code, compliant with the Federal Source Code Policy.

R

The development on this has moved to https://github.com/CDCgov/ww-inference-model

This repository analyzes viral genomes using Nextstrain to understand how SARS-CoV-2, the virus that is responsible for the COVID-19 pandemic, evolves and spreads. This is a copy of the original Nextstrain ncov repository, which will (by default) build augur all 50 states + DC + PR using the same parameters and subsampling strategy.

Data for the SPHERES Auspice site

Perl

HTML

This is the repository extending the Springfox Swagger UI package to meet CDC browser requirements.

Python

R

This project provides a tool for creating a global grid-based urban-rural classification to help estimate dog populations in support of mass vaccination campaign microplanning.

HTML

Python

Code to flag mentions of substance use disorder and mental health issues in clinical note text

R

surveytable: Formatted Survey Estimates

Jupyter Notebook

HTML

A little web tool to help people join data tables (without writing code!)

R

Algorithms for TB molecular epidemiology analysis

Template repository with rules, practices, and privacy, license, records notices to help people use the CDCgov GitHub organization.

HCL

Go

Groovy

JavaScript

Uncompromisingly Flexible Phylogenetic Trees in Javascript

Python

Tamura-Nei distance calculation

JavaScript

Tamura-Nei '93 Computation in Javascript

Shell

Python

🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission

Groovy

Bringing together healthcare providers by reducing the connection burden.

Python

U50 : measuring assembly output based on non-overlapping, target-specific contigs

C++

Bioinformatics related user-defined functions for Cloudera Impala.

Python

R

R

Vivli AMR Challenge submission

R

Wastewater-informed COVID-19 forecasting models submitted to the COVID-19 Forecast Hub

R

Python

HTML

Files for CDC EMEL GitHub

R

An in-development R package and a Bayesian hierarchical model jointly fitting multiple "local" wastewater data streams and "global" case count data to produce nowcasts and forecasts of both observations