Tree-based Correlation Screen and Visualization for Exploring Phenotype-Cell Type Association in Multiple Sample Single-Cell RNA-Sequencing Experiments
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Abstract
Single-cell RNA-seq experiments with multiple samples are increasingly used to discover cell types and their molecular features that may influence samples’ phenotype (e.g. disease). However, analyzing and visualizing the complex cell type-phenotype association remains nontrivial. TreeCorTreat is an open source R package that tackles this problem by using a tree -based cor relation screen to analyze and visualize the association between phenotype and tr anscriptomic f e atures a nd cell t ypes at multiple cell type resolution levels. With TreeCorTreat, one can conveniently explore and compare different feature types, phenotypic traits, analysis protocols and datasets, and evaluate the impacts of potential confounders.
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SciScore for 10.1101/2021.10.27.466024: (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 Limma [53] was then used to conduct differential expression analysis for each node as follows. Limmasuggested: (LIMMA, RRID:SCR_010943)COVID-19 PBMC single-cell RNA-seq data can be downloaded from the European Genome-Phenome Archive (EGA) and ArrayExpress database using the accession number: EGAS00001004571 and E-MTAB-9357. ArrayExpresssuggested: (ArrayExpress, RRID:SCR_002964)NSCLC dataset can be downloaded from the Gene Expression Omnibus under the accession number GSE176021. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Results from OddPub: Thank you for …
SciScore for 10.1101/2021.10.27.466024: (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 Limma [53] was then used to conduct differential expression analysis for each node as follows. Limmasuggested: (LIMMA, RRID:SCR_010943)COVID-19 PBMC single-cell RNA-seq data can be downloaded from the European Genome-Phenome Archive (EGA) and ArrayExpress database using the accession number: EGAS00001004571 and E-MTAB-9357. ArrayExpresssuggested: (ArrayExpress, RRID:SCR_002964)NSCLC dataset can be downloaded from the Gene Expression Omnibus under the accession number GSE176021. Gene Expression Omnibussuggested: (Gene Expression Omnibus (GEO, RRID:SCR_005012)Results from OddPub: Thank you for sharing your code and data.
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.
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