Discover CDCgov/phdi Open Source project

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens

phoenix

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

datasets-sars-cov-2

Perl

wastewater-informed-covid-forecasting

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

Rnssp

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.

mycosnp-nf

CDCgov/mycosnp-nf

Nextflow

cdc-open-viz

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

TypeScript

seqsender

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

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

template

tostadas

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

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

SARS-CoV-2_Genomic_Surveillance

ITF_Power_BI

openshift-fluentd-forwarder

Shell

TidyTree

Uncompromisingly Flexible Phylogenetic Trees in Javascript

Rt-without-renewal

Julia

NEDSS-Modernization

R interface to the CDC National Public Health Tracking Network API

EPHTrackR

aquascope

Nextflow

cdcgov.github.io

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

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

SaviR

covid_case_privacy_review

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

ww-inference-model

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

SDP-Vocabulary-Service

Repository for the SDP Vocabulary Service.

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.

opencdc

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

EPHTracking

SAS

PyRenew

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.

Rnssp-rmd-templates

cfa-gam-rt

R package for real-time Rt estimation with penalized splines

phdi-azure

Jupyter Notebook

MIRA

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

prime-fhir-converter

Kotlin

prime-simplereport-site

Landing / marketing site for the SimpleReport application

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

cdh-lava-react

CSS

NWSS

Data repository for NWSS

trusted-intermediary

Bringing together healthcare providers by reducing the connection burden.

Groovy

data-exchange-hl7

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

cfa-epinow2-pipeline

prime-central

Tamura-Nei '93 Computation in Javascript

mpx_networkmodel_mmwr

tn93.js

Sequence analysis and data visualization tool

MicrobeTrace-Archive

Algorithms for TB molecular epidemiology analysis

TB_molecular_epidemiology

data-exchange-fhir

cfa-viral-lineage-model

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

mycosnp

Shell

fdns-ui-react

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

MaRS

See Readme

Jupyter Notebook

CDC-Maps

cfa_azure

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)

measles-model-chicago-2024

spheres-augur-build

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.

prime-public-health-data-infrastructure

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.

HCL

patristic

A Phylogenetics toolkit for Javascript

Remove host contaminants from sequencing files

SanitizeMe

CDC collaboration on blockchain prototypes.

blockchain-collab

Data Ingestion for Modernization of NEDSS Project by Enquizit

data-exchange-upload

NEDSS-DataIngestion

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.

PoSE

Rnssp-shiny-apps

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

NLPWorkbench

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

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

fdns-ms-hl7-utils

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.

pynssp

Tamura-Nei distance calculation

tn93

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

fdns

blockchainTB

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

BMGAP

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

usa-sars-cov-2-nextstrain-sets

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

geneflow

Starter kit for use in creating new React projects

react-starter-kit

This repository contains an analysis pipeline developed to characterize WGS output

NCHHSTP-DTBE-Varpipe-WGS

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

National-Vital-Statistics-Mortality-Data

SAS

Opioid_SUD_MHI_MedCodes

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

Basic functionality for interacting with Azure from R

reportstream-sftp-ingestion

cfazuR

ixa

Rust

dibbs-query-connector

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

TypeScript

cfa-actions

A lightweight visualization for genetic sequence alignments

AlignmentViewer

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

SC2CLIA

Nextflow

cdc-react

TypeScript

Mia_publication

TSQL

EPHTracking-XMLGenerator

polkapox

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.

CDC_IIS_Open_Tools

surveytable: Formatted Survey Estimates

surveytable

excessdeathsCOVID19

phdi-google-cloud

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

Online Documentation for Rnssp R Markdown Templates

Rnssp-templates-docs

prime-devops

AMD-PGCoE

CDC-Data-Reconciliation-Tool