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21 Research products, page 1 of 3

  • Research software
  • 2018-2022
  • Open Source
  • Software
  • COVID-19

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  • Research software . 2020
    Open Source
    Authors: 
    Thams, Nikolaj Theodor; Jakobsen, Martin Emil; Mogensen, Phillip Bredahl; Lab, Copenhagen Causality;
    Publisher: bio.tools

    The dashboard provides tools for visualizing the COVID-19 spread in individual countries over time, as well as comparing different countries on a similar time scale. We provide time series of Danish test data. Furthermore, we have implemented an estimator for the actual...

  • Research software . 2021
    Open Source Groovy
    Authors: 
    Varona, Sarai; Monzón, Sara; Patel, Harshil; Ewels, Philip A.; Garcia, Maxime U.; Espinosa-Carrasco, Jose;
    Publisher: bio.tools

    nfcore/viralrecon is a bioinformatics analysis pipeline used to perform assembly and intra-host/low-frequency variant calling for viral samples. The pipeline supports short-read Illumina sequencing data from both shotgun (e.g. sequencing directly from clinical samples) ...

  • Research software . 2021
    Open Source R
    Authors: 
    Marchionni, Luigi;
    Publisher: bio.tools

    The package covid19census provides functions to extract COVID-19 cases, deaths, hospitalizations and test of U.S. and Italy at the county and regional level, respectively, and then combines them with other population metrics (age, sex, prevalence of chronic conditions, ...

  • Open Source
    Authors: 
    Gkiotsalitis, Konstantinos;
    Country: Netherlands

    Description:This repository contains the software code and the documentation of a model that sets the frequencies of public transport lines and derives the Pareto optimal demand management strategies considering the pandemic-imposed vehicle capacities due to COVID-19.Re...

  • Research software . 2021
    Open Source
    Authors: 
    Alser, Mohammed;
    Publisher: bio.tools

    COVIDHunter is an accurate and flexible COVID-19 outbreak simulation model that forecasts the strength of future mitigation measures and the numbers of cases, hospitalizations, and deaths for a given day, while considering the potential effect of environmental condition...

  • Open Source
    Authors: 
    Anton, Matei;
    Publisher: 4TU.ResearchData
    Country: Netherlands

    Code used together with its results for the paper as part of my Bachelor's Thesis project. The research consists of optimizing the kallisto algorithm for predicting the abundances of SARS-CoV-2 variants in wastewater samples. Specifically, I look at how only sequencing ...

  • Research software . 2021
    Open Source
    Authors: 
    Psomopoulos, Fotis E.;
    Publisher: bio.tools

    Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format).

  • Open Source
    Authors: 
    Cadena Pico, Jose; Soper, Braden; Ray, Pryadip; Mguyen, Chanh; Chan, Ryan;
    Publisher: DOE CODE

    Background: Machine learning (ML) based risk stratification models of Electronic Health records (EHR) data may help to optimize treatment of COVID-19 patients, but are often limited by their lack of clinical interpretability and cost of laboratory tests. We develop a ML...

  • Research software . 2021
    Open Source Python
    Authors: 
    Lu, Zhiyong;
    Publisher: bio.tools

    COVID-19-CT-CXR is a public database of COVID-19 CXR and CT images, which are automatically extracted from COVID-19-relevant articles from the PubMed Central Open Access (PMC-OA) Subset.

  • Open Source
    Authors: 
    Gkiotsalitis, Konstantinos;
    Publisher: 4TU.ResearchData
    Country: Netherlands

    Description:This repository contains the software code related to deriving dynamic service patterns in order to comply with the pandemic-imposed vehicle capacity limits in public transport operations.Currently, this repository contains:The model_case_study.py script whi...