Projects in Awesome Lists by CDCgov
A curated list of projects in awesome lists by CDCgov .
https://github.com/cdcgov/sars-cov-2_sequencing
A collection of sequencing protocols and bioinformatic resources for SARS-CoV-2 sequencing.
Last synced: 05 Apr 2025
https://github.com/cdcgov/prime-reportstream
ReportStream is a public intermediary tool for delivery of data between different parts of the healthcare ecosystem.
civic-tech fhir hl7 public-health
Last synced: 05 Apr 2025
https://github.com/cdcgov/phoenix
🔥🐦🔥PHoeNIx: a platform agnostic pipeline for healthcare-associated and antimicrobial resistant pathogens
Last synced: 07 Apr 2025
https://github.com/cdcgov/prime-simplereport
SimpleReport is a fast, free, and easy way for COVID-19 testing facilities to report results to public health departments.
graphql reactjs spring-boot terraform
Last synced: 05 Apr 2025
https://github.com/cdcgov/datasets-sars-cov-2
Benchmark datasets for WGS analysis of SARS-CoV-2. (https://peerj.com/articles/13821/)
bioinformatics public-health sars-cov-2
Last synced: 22 Apr 2025
https://github.com/cdcgov/wastewater-informed-covid-forecasting
Wastewater-informed COVID-19 forecasting models submitted to the COVID-19 Forecast Hub
Last synced: 19 Dec 2024
https://github.com/cdcgov/cdc-open-viz
CDC OpenViz is a library of React packages for data visualization.
data react visualization visualization-library
Last synced: 04 Apr 2025
https://github.com/cdcgov/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.
cdc essence essence-api nssp nssp-cop
Last synced: 19 Dec 2024
https://github.com/cdcgov/seqsender
Automated Pipeline to Generate FTP Files and Manage Submission of Sequence Data to Public Repositories
bioinformatics-pipeline biosample cdc cdc-influenza-division genbank gisaid gisaid-format gisaid-upload gisaid-uploader ncbi-biosamples ncbi-genbank ncbi-sra ncbi-submission ncird ncird-id seqsender sra
Last synced: 13 Apr 2025
https://github.com/cdcgov/template
Template repository with rules, practices, and privacy, license, records notices to help people use the CDCgov GitHub organization.
boilerplate collaboration governance guidance practices privacy records-management rules-of-behavior
Last synced: 21 Feb 2025
https://github.com/CDCgov/template
Template repository with rules, practices, and privacy, license, records notices to help people use the CDCgov GitHub organization.
boilerplate collaboration governance guidance practices privacy records-management rules-of-behavior
Last synced: 27 Nov 2024
https://github.com/cdcgov/tostadas
🧬 💻 TOSTADAS → Toolkit for Open Sequence Triage, Annotation and DAtabase Submission
azure bioinformatics conda docker genbank genetics liftoff metadata mpox ncbi nextflow nf-tower pipeline python rna-seq scicomp sequencing singularity sra vadr
Last synced: 15 Apr 2025
https://github.com/cdcgov/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
bayesian-inference cmdstanr forecasting hierarchical-models real-time-analytics stan wastewater-based-epidemiology
Last synced: 22 Apr 2025
https://github.com/cdcgov/cdcgov.github.io
Portal site for all CDCgov projects, https://cdcgov.github.io
cdc center-innovation collaboration discovery portal web
Last synced: 21 Feb 2025
https://github.com/cdcgov/ephtrackr
R interface to the CDC National Public Health Tracking Network API
cdc environmental-data epidemiology publichealth r rstats
Last synced: 22 Apr 2025
https://github.com/cdcgov/tidytree
Uncompromisingly Flexible Phylogenetic Trees in Javascript
Last synced: 22 Apr 2025
https://github.com/cdcgov/savir
The purpose of SaviR is to collect the functions needed to access and prepare various COVID data sources.
Last synced: 22 Apr 2025
https://github.com/cdcgov/mira
cdc-influenza-division genome-annotation genome-assembly influenza irma ncird-id quality-control rsv sars-cov-2
Last synced: 22 Apr 2025
https://github.com/cdcgov/pyrenew
Python package for multi-signal Bayesian renewal modeling with JAX and NumPyro.
epidemiology infectious-disease-models package renewal-process
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
center-innovation collaboration jekyll open-data open-source
Last synced: 22 Apr 2025
https://github.com/cdcgov/covid_case_privacy_review
Privacy review and statistical disclosure control methods for covid public case data.
coronavirus covid covid-19 privacy r sdc srrg
Last synced: 22 Apr 2025
https://github.com/CDCgov/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.
center-innovation collaboration jekyll open-data open-source
Last synced: 13 Apr 2025
https://github.com/cdcgov/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)
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
cdc essence essence-api nssp nssp-cop
Last synced: 22 Apr 2025
https://github.com/cdcgov/cfa-gam-rt
R package for real-time Rt estimation with penalized splines
Last synced: 22 Apr 2025
https://github.com/cdcgov/prime-simplereport-site
Landing / marketing site for the SimpleReport application
Last synced: 22 Apr 2025
https://github.com/cdcgov/trusted-intermediary
Bringing together healthcare partners by reducing the connection burden.
Last synced: 16 Apr 2025
https://github.com/cdcgov/prime-fhir-converter
The CDC’s Pandemic-Ready Interoperability Modernization Effort (PRIME) Java based FHIR conversion library
Last synced: 01 Jan 2025
https://github.com/cdcgov/cdh-lava-react
CDC Data Hub Lifecycle, Analysis & Visualization Accelerator (LAVA) REACT Components based on machine readable requirements.
agile-development azure data-analysis data-catalog data-governance data-quality data-science data-visualization databricks datavisualization devops excel-export metadata operations powerautomate powerbi pyspark security sql test-automation
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
Last synced: 22 Apr 2025
https://github.com/cdcgov/tb_molecular_epidemiology
Algorithms for TB molecular epidemiology analysis
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
Last synced: 16 Apr 2025
https://github.com/cdcgov/nlpworkbench
Natural Language processing for Pathology reports on cancer histology, laterality, side, and behavior.
usg-artificial-intelligence usg-natural-language-processing
Last synced: 21 Feb 2025
https://github.com/cdcgov/data-exchange-upload
The Public Health Data Operations (PHDO) Upload service provides secure ingestion, delivery, and observability of public health files from data senders to CDC program target locations via Application Programming Interfaces (APIs).
Last synced: 22 Apr 2025
https://github.com/cdcgov/sanitizeme
Remove host contaminants from sequencing files
Last synced: 22 Apr 2025
https://github.com/cdcgov/rnssp-shiny-apps
Rnssp Shiny Apps are custom-built applications with seamless integration to the Rnssp R package.
cdc essence essence-api nssp nssp-cop shiny shiny-apps
Last synced: 22 Apr 2025
https://github.com/cdcgov/cfa_azure
azure azure-batch azure-blob-storage azure-container-registry python
Last synced: 22 Apr 2025
https://github.com/cdcgov/pyrenew-hew
Models and infrastructure for forecasting COVID-19 and Flu hospitalizations using wastewater data with PyRenew
Last synced: 22 Apr 2025
https://github.com/cdcgov/fdns-ui-react
A collection of reusable React components for quickly building modern and accessible web applications.
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
Last synced: 21 Feb 2025
https://github.com/cdcgov/covid19-forecast-hub
A repository run by the US CDC to collect forecasts of weekly incident COVID-19 hospital admissions.
Last synced: 01 Jan 2025
https://github.com/cdcgov/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.
nextstrain-ncov spheres workflow
Last synced: 21 Feb 2025
https://github.com/cdcgov/geneflow
GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics
bioinformatics python workflow
Last synced: 22 Apr 2025
https://github.com/cdcgov/dynode
CDC/CFA/Predict/Scenarios ODE Modeling Framework
Last synced: 22 Apr 2025
https://github.com/cdcgov/forecasttools-py
A Python package for common pre- and post-processing operations done by CFA Predict for short term forecasting, nowcasting, and scenario modeling.
abstraction automation forecasting infectious-disease-modeling infrastructure
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
cdc essence essence-api nssp nssp-cop
Last synced: 22 Apr 2025
https://github.com/cdcgov/blockchain-collab
CDC collaboration on blockchain prototypes.
Last synced: 16 Apr 2025
https://github.com/cdcgov/bmgap
The Bacterial Meningitis Genome Analysis Platform, an analysis pipeline, ExpressJS API, and ReactJS webapp for the analysis and characterization of bacterial meningitis samples
Last synced: 22 Apr 2025
https://github.com/cdcgov/blockchaintb
Proof of project for CDC's r&d with using blockchain to support TB
Last synced: 21 Feb 2025
https://github.com/cdcgov/nchhstp-dtbe-varpipe-wgs
This repository contains an analysis pipeline developed to characterize WGS output
bioinformatics bioinformatics-pipeline genomics pipeline variant-annotations variant-calling
Last synced: 21 Feb 2025
https://github.com/cdcgov/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
Last synced: 22 Apr 2025
https://github.com/cdcgov/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.
Last synced: 21 Feb 2025
https://github.com/cdcgov/nedss-dataingestion
Data Ingestion for Modernization of NEDSS Project by Enquizit
Last synced: 22 Apr 2025
https://github.com/cdcgov/dibbs-query-connector
A FHIR client allowing public health agencies to query health care organizations directly or via a TEFCA QHIN
Last synced: 22 Apr 2025
https://github.com/cdcgov/surveytable
surveytable: Formatted Survey Estimates
estimates formatted-output pretty-print r survey tables
Last synced: 13 Apr 2025
https://github.com/cdcgov/react-starter-kit
Starter kit for use in creating new React projects
Last synced: 16 Apr 2025
https://github.com/cdcgov/cfazur
Basic functionality for interacting with Azure from R
Last synced: 22 Apr 2025
https://github.com/cdcgov/national-vital-statistics-mortality-data
Code for analyzing vital statistics mortality data, including death certificate literal text
Last synced: 21 Feb 2025
https://github.com/cdcgov/phfic-public-health-fhir-implementation-collaborative
Last synced: 22 Apr 2025
https://github.com/cdcgov/fdns
This is a central repository with high level information on Foundation Services, tutorials, example code, etc.
Last synced: 21 Feb 2025
https://github.com/cdcgov/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.
Last synced: 22 Apr 2025
https://github.com/cdcgov/alignmentviewer
A lightweight visualization for genetic sequence alignments
Last synced: 22 Apr 2025
https://github.com/cdcgov/data-exchange
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.
Last synced: 21 Feb 2025
https://github.com/cdcgov/sc2clia
An SARS-CoV-2 bioinformatics pipeline for CLIA validation using Dr. Erin Young's Cecret StaphB pipeline as a base
Last synced: 21 Feb 2025
https://github.com/cdcgov/phdi-google-cloud
Terraform and Python code for deploying PHDI pipelines to Google Cloud Platform.
Last synced: 22 Apr 2025
https://github.com/cdcgov/recordlinker
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.
Last synced: 22 Apr 2025
https://github.com/cdcgov/rnssp-templates-docs
Online Documentation for Rnssp R Markdown Templates
cdc documentation essence essence-api hugo nssp nssp-cop
Last synced: 22 Apr 2025
https://github.com/cdcgov/data-exchange-api-examples
This repository is for public documentation and examples for the CDC Enterprise Data Exchange (EDE/DEX) API
Last synced: 01 Jan 2025
https://github.com/cdcgov/hackathon2018
This is the repository for the projects from the 2018 Open CDC Hackathon
Last synced: 21 Feb 2025
https://github.com/cdcgov/influenza-generation_time-us
Estimating the generation time for influenza transmission using household data in the United States
Last synced: 01 Jan 2025