AnnotateMarkerGenes | Annotate differentially expressed genes using 'biomaRt'. |
ChoosePCs | Automatically choose the number of principal components. |
ComputeSilhouetteScores | Calculate the silhouette score of a clustering. |
ConvertGeneOrthologs | Convert a vector of MGI symbols to their HGNC orthologs and... |
CosineDist | Compute the cosine distance matrix. |
FindFilteredMarkers | Find marker genes for a given set of cells, and filter out... |
FindSpecificMarkers | Find highly specific marker genes for all clusters in a... |
FindSubpopulationMarkers | Identify marker genes for previously identified... |
IntegrateSubclusters | Integrate estimated subcluster identities into the original... |
PrepareData | Prepare scRNA-seq data for reclustering. |
ReclusterCells | Identify subpopulations in single cell clusters. |
ReduceDimensions | Run PCA / t-SNE / UMAP / PHATE. |
RunPHATE | Perform nonlinear dimension reduction using PHATE. |
theme_yehlab | A clean 'ggplot2' theme for dimension reduction plots. |
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