Comparative analysis of cell–cell communication at single-cell resolution
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SciScore for 10.1101/2022.02.04.479209: (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 Sentences Resources Data of longitudinal responses to SARS-CoV-2 infection in HBECs42 was downloaded from the Gene Expression Omnibus accession #GSE166766. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:One current limitation of Scriabin is that it does not take into account situations where multiple receptor subunits encoded by different genes are required in combination to respond to a ligand, or where receptor …
SciScore for 10.1101/2022.02.04.479209: (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 Sentences Resources Data of longitudinal responses to SARS-CoV-2 infection in HBECs42 was downloaded from the Gene Expression Omnibus accession #GSE166766. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:One current limitation of Scriabin is that it does not take into account situations where multiple receptor subunits encoded by different genes are required in combination to respond to a ligand, or where receptor subunits are known to differentially contribute to collective ligand-receptor avidity. An additional limitation is that Scriabin assumes uniform validity of ligand-receptor interactions in curated protein-protein interaction databases. Scriabin also treats all ligand-receptor pairs as equally important. In situations where it is known a priori which ligand-receptor pairs have a higher level of literature support, this information could be used to prioritize downstream analysis of particular ligand-receptor pairs. Similarly, all downstream signaling analyses in Scriabin rely on NicheNet’s ligand-target activity matrix, which may be biased by the cell types and stimulation conditions used to generate it. The NicheNet database also does not allow for analysis of inhibitory signaling, and thus Scriabin will only return CCC edges predicted to result in activated signaling. While Scriabin uses NicheNet to predict active CCC edges by examining downstream gene expression changes, an additional analysis goal includes identifying the upstream signaling machinery that results in the upregulation of a ligand or denotes successful signaling, as additional power could be gained by using sets of genes to infer upstream signaling rather than relying on ligand expression alone (whic...
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.
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