Discover CDCgov/wastewater-informed-covid-forecasting Open Source

🔥🐦🔥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

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

seqsender

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

phdi

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

cdc-open-viz

TypeScript

template

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

SARS-CoV-2_Genomic_Surveillance

openshift-fluentd-forwarder

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

ITF_Power_BI

TidyTree

Uncompromisingly Flexible Phylogenetic Trees in Javascript

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

tostadas

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

cdcgov.github.io

R interface to the CDC National Public Health Tracking Network API

EPHTrackR

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.

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.

Repository for the SDP Vocabulary Service.

SDP-Vocabulary-Service

aquascope

EPHTracking

NEDSS-Modernization

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.

phdi-azure

Jupyter Notebook

prime-fhir-converter

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

Kotlin

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

prime-simplereport-site

Landing / marketing site for the SimpleReport application

prime-central

Gold Idea First Templates covering data, analytics and visualization.

mpx_networkmodel_mmwr

gift

tn93.js

Tamura-Nei '93 Computation in Javascript

Sequence analysis and data visualization tool

NWSS

Data repository for NWSS

MicrobeTrace-Archive

Rt-without-renewal

Julia

mycosnp

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

fdns-ui-react

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

CDC-Maps

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.

MaRS

See Readme

Jupyter Notebook

spheres-augur-build

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

trusted-intermediary

Bringing together healthcare providers by reducing the connection burden.

Groovy

MIRA

A Phylogenetics toolkit for Javascript

patristic

Remove host contaminants from sequencing files

SanitizeMe

CDC collaboration on blockchain prototypes.

blockchain-collab

R package for real-time Rt estimation with penalized splines

data-exchange-fhir

cfa-gam-rt

NEDSS-DataIngestion

Data Ingestion for Modernization of NEDSS Project by Enquizit

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

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

Rnssp-shiny-apps

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

TB_molecular_epidemiology

Algorithms for TB molecular epidemiology analysis

geneflow

GeneFlow: A Workflow Engine for Bioinformatics and Public Health Analytics

usa-sars-cov-2-nextstrain-sets

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

National-Vital-Statistics-Mortality-Data

SAS

AlignmentViewer

A lightweight visualization for genetic sequence alignments

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

Mia_publication

TSQL

SC2CLIA

Nextflow

ITF-Dashboard

A code-only repo of the ITF Dashboard backend

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.

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

excessdeathsCOVID19

phdi-google-cloud

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

Online Documentation for Rnssp R Markdown Templates

Rnssp-templates-docs

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

prime-devops

AMD-PGCoE

Opioid_SUD_MHI_MedCodes

Repository for CDC's Surveillance Data Platform project.

data-exchange-hl7-dbx

SET-NET

MicrobeTraceNext

prime-data-input-api

SDP

Jinja

fdns-ms-rules

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

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

nncc

fdns-ms-cda-utils

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

FreeMarker

EPHTracking-XMLGenerator

savimpx

MPX Helper Functions for the Situational Awareness and Visualization Team

fdns-ms-gateway

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

Example UI for a Datalake Dashboard

Crypto_gp60_Subtyping_Tool

Perl

ex-ui-datalake-dashboard

WDPB_CDS_PHL_Tools

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.

data-exchange-upload

legionella_pneumophila_genomics

Python package for statistical inference and forecast of epi models using multiple signals

multisignal-epi-inference

This repository is created for NEDSS Helm charts.

concept-dictionary-manager

NEDSS-Helm

SDP-CBR

cdc-react

EPHTracking-RAD

legionella_pneumophila_SBT_analysis