Welcome to the GitHub repository of the COVID-19 Complement Atlas. This repository contains the R code and raw data behind complementatlas.com, an interactive portal for exploring complement dysregulation during COVID-19. The data underlying this project have also been deposited on Zenodo and Dryad.
For the methods and results, please read the full paper: A Complement Atlas identifies interleukin 6 dependent alternative pathway dysregulation as a key druggable feature of COVID-19.
The patient samples and clinical data utilized in this project were collected during three randomized clinical trials conducted in the 2020 COVID-19 pandemic:
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Effect of anti-interleukin drugs in patients with COVID-19 and signs of cytokine release syndrome (COV-AID): A factorial, randomized, controlled trial (Declercq et al., 2021).
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Loss of GM-CSF-dependent instruction of alveolar macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment (SARPAC) (Bosteels et al., 2022).
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Efficacy and safety of the investigational complement C5 inhibitor zilucoplan in patients hospitalized with COVID-19: an open-label randomized controlled trial (ZILUCOV) (De Leeuw et al., 2022).
This repository includes the following files:
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ui.R, server.R, and runShinyApp.R are scripts to launch the Complement Atlas website.
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data_loading.R is responsible for loading all the raw data.
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plot_functions.R defines various functions for data visualization.
Additionally, the www subfolder contains all the data in CSV format, along with some visuals.
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complement.csv contains the complement level dataset.
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complement_anti_C5.csv holds the levels of sC5b-9 upon anti-C5 therapy.
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complement_function.csv contains the ex vivo complement functional tests.
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olink.csv includes the 3000-plex proteomics dataset.
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README.txt includes metadata for the above files.
The code in this repository is released under the MIT license. Please refer to the LICENSE file for more information.
If you have any questions or suggestions regarding the Complement Atlas, please contact us at karel.vandamme@ugent.be or bart.lambrecht@ugent.be.
Thank you for your interest in the Complement Atlas!