1. SciScore for 10.1101/2021.11.24.21266741: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    NIH rigor criteria are not applicable to paper type.

    Table 2: Resources

    Software and Algorithms
    Study data were collected and managed using REDCap electronic data capture tools hosted at Centro de Investigación Biomédica en Red (CIBER) [57, 58] (Supplementary Note).
    suggested: (REDCap, RRID:SCR_003445)
    First, a list of probe sets was removed based on poor cluster separation or excessive minor allele frequency (MAF) difference from The 1000 Genomes Project data (1KGP) [59].
    1000 Genomes Project
    suggested: (1000 Genomes Project and AWS, RRID:SCR_008801)
    Ancestry was then inferred with Admixture [63] using the defined 1KGP superpopulations.
    suggested: (ADMIXTURE, RRID:SCR_001263)
    Then, the main results of both Spanish cohorts (SCOURGE and CNIO) for the overall and sex-stratified analyses were meta-analysed assuming a fixed-effects model using METAL [68].
    suggested: (METAL, RRID:SCR_002013)
    VEP (https://www.ensembl.org/info/docs/tools/vep/index.html) and the V2G aggregate scoring from Open Targets Genetics (https://genetics.opentargets.org) were used to annotate the most prominent biological effects of the variants in the credible sets.
    suggested: None
    ROH calling: The ROH segments longer than 300 Kb were called in SCOURGE using PLINK 1.9 in the European QC-ed genotyped dataset (before imputation) with the following parameters: homozyg-snp 30, homozyg-kb 300, homozyg-density 30, homozyg-window-sn 30, homozyg-gap 1000, homozyg-window-het 1, homozyg-window-missing 5, homozyg-window-threshold 0.05.
    suggested: (PLINK, RRID:SCR_001757)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.

    Results from TrialIdentifier: We found the following clinical trial numbers in your paper:

    NCT04374279WithdrawnTrial to Promote Recovery From COVID-19 With Endocrine Thera…
    NCT04397718CompletedHormonal Intervention for the Treatment in Veterans With COV…
    NCT04345887CompletedSpironolactone in Covid-19 Induced ARDS

    Results from Barzooka: We found bar graphs of continuous data. We recommend replacing bar graphs with more informative graphics, as many different datasets can lead to the same bar graph. The actual data may suggest different conclusions from the summary statistics. For more information, please see Weissgerber et al (2015).

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • No funding statement was detected.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

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