Man pages for jn-goe/gruffi
Gruffi identifies and removes stressed cells from brain organoid single-cell datasets.
| AddCustomScore | AddCustomScore |
| AddGOGeneList.manual | AddGOGeneList.manual |
| AddGOScore | AddGOScore |
| AssignGranuleAverageScoresFromGOterm | Assign granule average scores from Gene Ontology (GO) terms. |
| AutoFindGranuleResolution | AutoFindGranuleResolution |
| CalcClusterAverages_Gruffi | Calculate Cluster Averages for Granules in a Seurat Object |
| CalcStandDevSkewedDistr | Calculate Standard Deviation for Skewed Distributions |
| CalcTranscriptomePercentage | CalcTranscriptomePercentage |
| CalcTranscriptomePercentageGO | CalcTranscriptomePercentageGO |
| CalculateAndPlotGoTermScores | Calculate and Plot GO Term Scores |
| CalculateMedianClusterSize | Calculate Median Cluster Size |
| CleanDuplicateScorenames | CleanDuplicateScorenames |
| ClearGruffi | Remove gruffi results from the Seurat object |
| ClusterUMAPthresholding | ClusterUMAPthresholding |
| CustomScoreEvaluation | CustomScoreEvaluation |
| dot-convert.GO_term.2.score | .convert.GO_term.2.score |
| dot-convert.score.2.GO_term | .convert.score.2.GO_term |
| dot-fix.metad.colname.rm.trailing.1 | .fix.metad.colname.rm.trailing.1 |
| dot-parse.GO | Parse GO Term from Granule-score Name |
| dot-round | Safe Rounding Function |
| FeaturePlotSaveCustomScore | FeaturePlotSaveCustomScore |
| FeaturePlotSaveGO | FeaturePlotSaveGO |
| FilterStressedCells | Filter Stressed Cells from a Seurat Object |
| FindThresholdsAuto | Automated GO Term-based Thresholding without using a Shiny... |
| FindThresholdsShiny | Launch Shiny App for GO Term-based Thresholding |
| GetAllGOTermNames | Show All GO Terms in an Object, and retrieve corresponding... |
| GetGOTerms | Retrieve Gene Ontology (GO) Terms and Associated Genes |
| GetGruffiClusteringName | Retrieve First Clustering Run or First Matching Pattern Run |
| GrScoreHistogram | Histogram Visualization of Granule Scores with Threshold |
| GrScoreUMAP | Wrapper for clUMAP with Thresholding and Plotting |
| IntersectWithExpressed | IntersectWithExpressed |
| ParseGruffiGranuleScoreName | Generate Gruffi Granule Score Name |
| PlotClustSizeDistr | PlotClustSizeDistr |
| PlotNormAndSkew | PlotNormAndSkew |
| ReassignSmallClusters | ReassignSmallClusters |
| StressBarplotPerCluster | Stress Barplot Per Cluster |
| StressUMAP | Wrapper for clUMAP with Thresholding and Plotting |
| UMAP3Dcubes | UMAP3Dcubes |
