Single-cell landscape of bronchoalveolar immune cells in patients with COVID-19
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
No abstract available
Article activity feed
-
SciScore for 10.1101/2020.02.23.20026690: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Healthy Control Data: The lung scRNA-seq data from the healthy controls was acquired from the Gene Expression Omnibus (GEO) database under the series number GSE122960 [12], which contains data of lung tissue from eight lung transplant donors generated using 3’ V2 chemistry kit on Chromium Single cell controller (10xGenomics). Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Specifically, splicing-aware aligner STAR [30] was used in FASTQs … SciScore for 10.1101/2020.02.23.20026690: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Healthy Control Data: The lung scRNA-seq data from the healthy controls was acquired from the Gene Expression Omnibus (GEO) database under the series number GSE122960 [12], which contains data of lung tissue from eight lung transplant donors generated using 3’ V2 chemistry kit on Chromium Single cell controller (10xGenomics). Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Specifically, splicing-aware aligner STAR [30] was used in FASTQs alignment. STARsuggested: (STAR, RRID:SCR_015899)Differential analysis for clusters: MAST [32] in Seurat v3 was used to perform differential analysis. MASTsuggested: (MAST, RRID:SCR_016340)Single cell trajectory analysis: Slingshot [33] was used to perform pseudotime inference for the four myeloid cell groups. Slingshotsuggested: (Slingshot, RRID:SCR_017012)Regulatory network inference: Single cell regulatory network for 4 myeloid groups was constructed with SCENIC [34]. SCENICsuggested: (SCENIC, RRID:SCR_017247)), KEGG pathway analyses and Gene Set Enrichment Analysis (GSEA) [35] were performed with clusterProfiler [36], which supports statistical analysis and visualization of functional profiles for genes and gene clusters. KEGGsuggested: (KEGG, RRID:SCR_012773)clusterProfilersuggested: (clusterProfiler, RRID:SCR_016884)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.
-
-
