CDCgov/ww-inference-model

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R
License
Apache License 2.0
Created 5 months ago
Updated 28 days ago

CDCgov/ww-inference-model

CDCgov

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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

SARS-CoV-2_Sequencing

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

prime-reportstream

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

covid19healthbot

[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.

prime-simplereport

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

phoenix

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

datasets-sars-cov-2

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

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

phdi

cdc-open-viz

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

seqsender

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

template

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

tostadas

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

SARS-CoV-2_Genomic_Surveillance

ITF_Power_BI

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

openshift-fluentd-forwarder

TidyTree

Uncompromisingly Flexible Phylogenetic Trees in Javascript

Rt-without-renewal

NEDSS-Modernization

EPHTrackR

R interface to the CDC National Public Health Tracking Network API

aquascope

cdcgov.github.io

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

SaviR

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

covid_case_privacy_review

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

SDP-Vocabulary-Service

Repository for the SDP Vocabulary Service.

opencdc

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.

EPHTracking

PyRenew

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

Rnssp-rmd-templates

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.

cfa-gam-rt

R package for real-time Rt estimation with penalized splines

phdi-azure

Jupyter Notebook

MIRA

prime-fhir-converter

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

prime-simplereport-site

Landing / marketing site for the SimpleReport application

cdh-lava-react

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

NWSS

Data repository for NWSS

trusted-intermediary

Bringing together healthcare providers by reducing the connection burden.

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.

cfa-epinow2-pipeline

prime-central

mpx_networkmodel_mmwr

tn93.js

Tamura-Nei '93 Computation in Javascript

MicrobeTrace-Archive

Sequence analysis and data visualization tool

TB_molecular_epidemiology

Algorithms for TB molecular epidemiology analysis

data-exchange-fhir

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.

cfa-viral-lineage-model

mycosnp

fdns-ui-react

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

MaRS

Jupyter Notebook

CDC-Maps

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

cfa_azure

measles-model-chicago-2024

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)

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.

patristic

A Phylogenetics toolkit for Javascript

SanitizeMe

Remove host contaminants from sequencing files

blockchain-collab

CDC collaboration on blockchain prototypes.

data-exchange-upload

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.

NEDSS-DataIngestion

Data Ingestion for Modernization of NEDSS Project by Enquizit

PoSE

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.

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.

fdns-ms-hl7-utils

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

pynssp

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.

tn93

Tamura-Nei distance calculation

fdns

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

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

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

react-starter-kit

Starter kit for use in creating new React projects

NCHHSTP-DTBE-Varpipe-WGS

This repository contains an analysis pipeline developed to characterize WGS output

National-Vital-Statistics-Mortality-Data

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

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

reportstream-sftp-ingestion

cfazuR

Basic functionality for interacting with Azure from R

ixa

dibbs-query-connector

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

cfa-actions

AlignmentViewer

A lightweight visualization for genetic sequence alignments

SC2CLIA

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

cdc-react

Mia_publication

EPHTracking-XMLGenerator

polkapox

CDC_IIS_Open_Tools

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.

surveytable

surveytable: Formatted Survey Estimates

excessdeathsCOVID19

phdi-google-cloud

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

Rnssp-templates-docs

Online Documentation for Rnssp R Markdown Templates

prime-devops

AMD-PGCoE

CDC-Data-Reconciliation-Tool

spatialwwinference

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

influenza-generation_time-us

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

SET-NET

Jupyter Notebook

MicrobeTraceNext

prime-data-input-api

SDP

Repository for CDC's Surveillance Data Platform project.