Man pages for kordastilab/ImmunoCluster
Fast and accesible Immune profiling CyTOF data
| biaxial_plot | Generate a biaxial dot plot with contouring of the SCE data |
| density_plot | Generate a density plot of a dimensionality reduction of the... |
| imc_rank | Creates a ranked heatmap based on SingleCellExperiment object |
| markerExpression | Generate an dotplot of a dimensionality reduction with marker... |
| mdsplot | Create sample-level MDS plot |
| performTSNE | Perform TSNE dimensionality reduction on SingleCellExperiment... |
| performUMAP | Perform UMAP dimensionality reduction on SingleCellExperiment... |
| plotAbundance | Create a ggplot object of sce cluster proportion abundances... |
| processFCS | Import .fcs file data into a 'SingleCellExperiment' object... |
| runFlowSOM | Perform combined FlowSOM clustering followed by consensus... |
| runPhenograph | run Rphenograph implementation from... |
| setClusterIdents | Relabel clustering identities in sce metadata. |
| stat_test_clust | Perform statistical test on cluster abundances as a... |
| stat_test_expression | Perform statistical test on median expression values across... |
| subset_sce_metadata | Subset the sce object based on a column of the metadata table |
| volcanoPlot | Generate a volcano plot using statistical testing output |
| write_sce_to_fcs | Export an SCE to.fcs format |
