In naikai/sake: Single-cell RNA-Seq Analysis and Klustering Evaluation
Differential expression (DE) analysis between NMF clusters allows for the identification of additional genes differentially expressed in each NMF cluster with statistical analyses calculated via the DESeq algorithm (Love et al., 2014). Expression distributions for DE genes across NMF groups are displayed together with RefSeq annotation.
Differential Expression
Enrichment Analysis
GO Term enrichments allow for the identification of functional categories enriched in each NMF cluster, which can serve as guidance for further investigation and follow up studies.
Note: Make sure to select the correct species. SAKE currently supports Human and Mouse.
Summary table and plots for the enrichment analysis.
User can also click on one of the enriched KEGG pathways they are interested in. Pathview will maps and renders pathway grpahs. In this case, we select TGF-beta signaling pathway from NMF Group3. Red color indicates genes that are upregulated in selected NMF cluster as compared to all the other clusters.
naikai/sake documentation built on Feb. 15, 2023, 11 p.m.
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Differential expression (DE) analysis between NMF clusters allows for the identification of additional genes differentially expressed in each NMF cluster with statistical analyses calculated via the DESeq algorithm (Love et al., 2014). Expression distributions for DE genes across NMF groups are displayed together with RefSeq annotation.
Differential Expression
Enrichment Analysis
GO Term enrichments allow for the identification of functional categories enriched in each NMF cluster, which can serve as guidance for further investigation and follow up studies.
Note: Make sure to select the correct species. SAKE currently supports Human and Mouse.
Summary table and plots for the enrichment analysis.
User can also click on one of the enriched KEGG pathways they are interested in. Pathview will maps and renders pathway grpahs. In this case, we select TGF-beta signaling pathway from NMF Group3. Red color indicates genes that are upregulated in selected NMF cluster as compared to all the other clusters.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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