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21 Research products, page 1 of 3

  • Research software
  • 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...

  • 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...

  • 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, ...

  • 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...

  • 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.

  • Research software . 2021
    Open Source Python
    Authors: 
    Safta, Cosmin; Ray, Jaideep; Blonigan, Patrick; Chowdhary, Kenny;
    Publisher: DOE CODE

    SAND2021-0565 O PRIME is a modeling framework designed for the real-time characterization and forecasting of partially observed epidemics. The method is designed to help guide medical resource allocation in the early epoch of the outbreak. Characterization is the estima...

  • Research software . 2021
    Open Source C++
    Authors: 
    Pucci, Fabrizio; Rooman, Marianne;
    Publisher: bio.tools

    SpikePro algorithm predicts the fitness of a SARS-CoV-2 strain from the sequence of its spike protein. Given the target sequence in fasta format, the algorithm aligns it to the reference SARS-CoV-2 spike protein, list all mutations with respect to the reference and comp...