Enrichment analysis on regulatory subspaces: A novel direction for the superior description of cellular responses to SARS-CoV-2

  1. Pedro Rodrigues
  2. Rafael S. Costa
  3. Rui Henriques

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  1. Version published to 10.1016/j.compbiomed.2022.105443
  2. ScreenIT

    SciScore for 10.1101/2021.12.15.472466: (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
    SentencesResources
    Additionally, EnrichR web tool provides access to multiple knowledge bases (https://maayanlab.cloud/Enrichr/libraries).
    EnrichR
    suggested: (Enrichr, RRID:SCR_001575)
    Additionally, we use the Kyoto Encyclopedia of Genes and Genomes (KEGG) [32] to analyse enriched pathways and diseases.
    KEGG
    suggested: (KEGG, RRID:SCR_012773)
    : Python version 3.8, NumPy, pandas, scikit-learn and matplotlib libraries.
    Python
    suggested: (IPython, RRID:SCR_001658)
    NumPy
    suggested: (NumPy, RRID:SCR_008633)
    matplotlib
    suggested: (MatPlotLib, RRID:SCR_008624)

    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: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    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.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • 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.

  3. Version published to 10.1101/2021.12.15.472466v1 on bioRxiv