Man pages for guokai8/scGSVA
GSVA and UCell signature enrichment analysis for single cell RNA seq
| Annot-class | Class "Annot" This class represents the Annotation... |
| buildAnnot-methods | make annotation database |
| buildMSIGDB | Download database from Msigdb and prepare for enrichment... |
| distcolor | distinguish colors for making figures |
| dot-do_aov | do anova test and return results as data.frame |
| dot-do_ttest | do t.test |
| dot-do_wilcox | do wilcox test |
| dot-getann | build annotaion for kegg |
| dot-getmsig | msigdb support species |
| dot-get.quantile | get the quantile of data |
| dot-makeGOdata | Build GO annotation |
| dot-makeKOdata | Build KEGG annotation |
| dot-makeKOMdata | make KEGG module annotation data function |
| dot-makeROdata | Build Reactome annotation data |
| dotPlot | DotPlot for the specific pathway |
| featurePlot | Visualize 'Pathways or Terms' on a dimensional reduction plot |
| findPathway | Fit linear model for each pathway |
| genes-GSVA-method | gene method |
| genes-methods | gene method |
| GSVA-class | Class "GSVA" This class represents the Annotation information |
| Heatmap | Generate heatmap for the enrichment scores |
| idconvert | Convert id between different type |
| lightcolor | light colors for making figures |
| msigdbinfo | Print MSIGDB infomation |
| pbmc | A small example version of the PBMC dataset |
| pbmcs | A small example version of the PBMC dataset |
| ridgePlot | Generate a ridge plot to examine enrichment distributions |
| sce_small | Small SingleCellExperiment object |
| scgsva | GSVA function for single cell data or data.frame with... |
| set.cut.off | modified from Seurat github transform data with the min and... |
| showData | show avaliable data based on bioconductor annotation package |
| sigPathway | Significance testing between groups. |
| spatialFeaturePlot | Visualize 'Pathways or Terms' on a Spatial plot |
| split.data.matrix | Split data matrix into smaller sub-matrices ('chunks') |
| subset.GSVA | subset the GSVA object |
| vlnPlot | VlnPlot for the pathways |
