COVID-19 workflows and datasets.

Processing workflow for COVID-19 single cell data

This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Can Liu, Andrew J. Martins, William W. Lau, Nicholas Rachmaninoff, ..., John S. Tsang. "Time-resolved Systems Immunology Reveals a Late Juncture Linked to Fatal COVID-19" Cell (2021), In press.

🦠 Corona Time: An Alfred Workflow For Tracking COVID-19

Reproducible reporting workflows for the immune correlates statistical analyses of the Moderna and Janssen COVID-19 vaccine efficacy trials by the USG/COVE Response Biostatistics Team [Archived 16 October 2021]

This repository consists of scripts and workflows used for generating results, figures, and tables published in the article: Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19.

Workflows for viral analysis (as part of COVID-19 Biohackathon)

This repository hosts research project on Airbnb business in COVID-19 era. The ownership of this repository belongs to Team 5. All project content solely serves the learning goals of Data Preparation and Workflow Management (dPrep) course.

Workflows and containers for processing COVID-19 data.

A workflow to automate the annotation of newick trees for COVID-19

This repository is dedicated to the scoring of lung diseases, where we propose a two-step workflow used for segmentation and scoring of lung diseases, including COVID-19

This is a public repository of code linked to the 'Multisite Implementation of a Workflow-Integrated Machine Learning System to Optimize COVID-19 Hospital Admission Decisions' publication in npj Digtal Medicine.

This project automates the process of marking student attendance from Zoom meeting screenshots using Optical Character Recognition (OCR). Originally developed during the COVID-19 lockdown for remote classes, it removes the manual effort of scanning participant names and speeds up the daily attendance workflow.

Coordinating the CWL workflow related to the 2020 COVID-19 BioHackathon

COVID-19 multiscale modelling of the virus and patients’ tissue

Workflow to pull, convert, clean and categorize data from the official website with COVID-19 cases in Massachusetts

Scanpy pipeline analyzing COVID-19 lung scRNA-seq. Full workflow from QC to pathway analysis with Snakemake. Identifies macrophage/NK cell signatures in severe infection. Adaptable to other disease studies.

Source code and data repository to build a COVID-19 specific DTI-HHI-HPI network in Neo4j database. This repository is associated with the study disclosed in manuscript: Zahoranszky-Kohalmi et al., A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research.

Filtering Covid-19 Data from various data sources listed in HealthData and automating the workflow using Apache Airflow

COVID-19 Molecular Diagnostics: An Aquarium Workflow

A Snakemake workflow for visualising UK Covid-19 data

Workflow Project to Create Maps of US COVID-19 Cases

A COVID-19 early/secondary detection prototype UI and workflow

Python workflow to design COVID-19 primers and assess their specificity and amplicon RNA secondary structure stability.

An extension to the C-VIEW (COVID-19 VIral Epidemiology Workflow) pipeline that uses Freyja to identify variants and lineages prevalent in mixed-input samples like wastewater.

A deep learning pipeline for COVID-19 detection from cough and breath audios, featuring preprocessing, feature extraction, and end-to-end training workflows. Includes a custom Hugging Face dataset and support for transformer and CNN-based audio models.

Analysis pipeline for single-cell RNA sequencing (scRNA-seq) data focused on T cells in COVID-19. Includes scripts and workflows for data processing, visualization, and identifying immune cell signatures and responses. Designed to accelerate reproducible research in immunology and single-cell genomics.

These notebooks enable the interactive development of topic-modeling on the the COVID-19 research-text which has been made available by the White House as of 2020-03-16. After generating the processed outputs of the raw text using the CORD-19 Data Processing notebook, the user is simply required to input their directory (using the text boxes embedded in the Notebook) to read-in the pre-processed data before making their topic-modeling selections. This workflow is designed for anyone looking to leverage Python to explore and analyze the COVID-19 text.

Hospice facility aims at improving the lives of patients suffering from terminal illness. Our system includes 24*7 access to Providers, Nurses, and Counsellors for their diagnosis and treatment via a centralized system and database. The system also involves healthcare claims, donations, and audit logging for all financial transactions. Lastly, it also has in-built important workflows used to fight the epidemic, COVID-19 including a self-diagnosis form for a patient and provision to schedule a COVID-19 Test as well.

This repository contains various workflows and scripts for analyzing and visualizing COVID-19 data, including confirmed cases, deaths, and vaccinations. The project is organized into multiple workflows, each focusing on a specific aspect of the COVID-19 pandemic.