Man pages for jgarces02/FlowCT
A semi-automated workflow for deconvolution of immunophenotypic data and objective reporting on large datasets
| asciify | Convert table to ASCII format |
| as.flowSet.SE | Transform a 'fcs.SCE' object into a 'flowset' object |
| barplot.cell.pops | Stacked barplot with cell clusters |
| batch.removal | Remove batch effect |
| boxplot.cell.clustering | Boxplots for identified clusters |
| cell.count.bx | Boxplot according according metadata |
| circ.tree | Circular dendrogram tree |
| clustering.flow | Clustering FCS data |
| clusters.rename | Rename clusters from numeric to cell name |
| col.annot.pheatmap | Create a palette of colors suitable for doing a heatmap |
| combine.subclusterings | Combine multiple subclustering with initial one |
| corplot.conditions | Draw a correlation heatmap between two conditions |
| cox.plot | Forest plot for uni/multivariable Cox regressions |
| dim.reduction | Calculate dimensional reductions |
| div.colors | Create a palette of colors |
| dotplot.DE | Differential expression plot to identify populations within... |
| dr.plotting | Plot DR data |
| dumbPlot | Dumbbell plot with clusters |
| export.metaFCS | Create FCS from a 'fcs.SCE' object |
| fcs.SCE | Read multiple FCS files and create a 'fcs.SCE' object |
| flowplot | Draw expression dotplots |
| marker.names | Show and change markers names |
| marker.normalization | Normalization for markers' expression |
| median.dr | Calculate a DR with median values |
| median.heatmap | Heatmap from median expression values |
| median.values | Obtain median values |
| multicox | Multivariable Cox Regression |
| multidensity | Density plots with expression values overlapped |
| parallel.plot | Longitudinal differential dotplot |
| pop.cutoff | Determine optimal cutoffs for immune populations |
| prog.pop.selection | Determine populations with prognostic value |
| qc.and.removeDoublets | Perform quality control and remove doublets |
| read.FCSset | Load multiple FCS files |
| remove.pop | Delete a population from a 'fcs.SCE' object -> DEPRECATED... |
| rpart.tree | Recursive partitioning tree |
| scale.exprs | Scale expression |
| sc.heatmap | Heatmap at event-level |
| scMetadata.fromFCS | Create a single-event metadata |
| sub.samples | Reduce the nummber of events of a 'fcs.SCE' object |
| surv.plot | Survival plots according cell cutoffs |
| surv.tree | Kaplan-Meier from survival tree |
| unicox | Univariable Cox Regression |
| unify.FCSheaders | Unify all FCS header for multiple FCS |
