Man pages for MattPM/scglmmr
Sample-level Single-cell Generalized Linear Multilevel Models in R
| AggregateCellMetadata | AggregateCellMetadata - take cell level metadata and collapse... |
| AverageSampleModuleZscore | AverageSampleModuleZscore apply the function... |
| BulkDesignMatrix | BulkDesignMatrix - designmatrix for the main experiment... |
| calc_avg_module_zscore | calc_avg_module_zscore - calculate average module z score of... |
| CombineResults | CombineResults - For all cell types merge the gsea leading... |
| EnrichmentJaccard | EnrichmentJaccard - using gsea list and LeadingEdgeIndexed... |
| ExtractResult | ExtractResult - convenience function to return statistics for... |
| FgseaList | FgseaList - wrapper around fast gene set enrichment analysis... |
| FitDream | FitDream - run mixed effects model on aggregated (summed)... |
| FitLmer | FitLmer - This is a simpler version of FitLmerContrast that... |
| FitLmerContrast | FitLmerContrast - for data with pre post treatment and 2... |
| GetContrastResults | GetContrastResults - return results from a contrast fit on... |
| GetContrastResultsRaw | GetContrastResultsRaw - calculate p values and return... |
| GetGeneMatrix | GetGeneMatrix get a gene matric for plotting genes by... |
| GetLeadingEdgeFull | GetLeadingEdgeFull Get a tidy dataframe of ALL Leading Edge... |
| GetLeadingEdgeGenes | GetLeadingEdgeGenes get the leading edge genes from a single... |
| GetRankResults | GetRankResults get list of gene ranks by t stat for fGSEA |
| GetRankResultsRaw | GetRankResultsRaw get list of gene ranks by raw t statistic... |
| GetTidySummary | GetTidySummary - tidy data summary for a single cell type |
| GSEABarPlot | GSEABarPlot - plot gsea results for a single cell type |
| GSEABubblePlot | GSEABubblePlot plot gsea results for all cell types |
| HeatmapDiag | HeatmapDiag utility function for 'pheatmap' using 'slanter'... |
| LeadEdgeSampleHeatmap | LeadEdgeSampleHeatmap make a heatmap of average expression... |
| LeadEdgeTidySampleExprs | LeadEdgeTidySampleExprs - convert a PseudobulkList into a... |
| LeadingEdgeIndexed | LeadingEdgeIndexed - extract leading edge genes from... |
| Normalize | Normalize - normalize summed gene counts across samples. This... |
| NormalizePseudobulk | NormalizePseudobulk |
| pipe | Pipe operator |
| PlotFgsea | PlotFgsea identical to GSEABubblePlot, returns plot for... |
| PlotGeneDistCohort | PlotGeneDistCohort |
| PlotHypergeometric | PlotHypergeometric - plot results returned by... |
| PseudobulkList | PseudobulkList - make a pseudobuk summed or average dataset... |
| RbindGseaResultList | RbindGseaResultList - prepare gsea result list for... |
| RunFgseaOnRankList | RunFgseaOnRankList - wrapper around fast gene set enrichment... |
| RunHypergeometricTest | RunHypergeometricTest - run a hypergeometric test on results... |
| RunVoomLimma | RunVoomLimma |
| RunVoomLimma_covar | RunVoomLimma_covar RunLimmaVoom with an option to adjust for... |
| SCMixedPoisson | SCMixedPoisson - Fit a gene level Poisson count mixed... |
| SubjectCelltypeTable | SubjectCelltypeTable - quality control on sample level... |
| TidySampleData | TidySampleData convert data from PseudobulkList into a... |
| WeightedCellModuleScore | WeightedCellModuleScore - calculate the average or weighted... |
