Man pages for astrolabediagnostics/orloj
Utilities for the Astrolabe Diagnostics platform
| addBackticks | Add backticks to a string. |
| astrolabeDebrisLabels | Astrolabe debris labels. |
| beadChannelNames | Bead channel names. |
| calculateFcsDigest | Calculate parameter digest for sample. |
| citeseqPreprocess | Preprocess citeseq sample. |
| convertFlowFrame | Convert a FlowCore flow_frame to Astrolabe sample. |
| differentialAbundanceAnalysis | Differential abundance analysis. |
| experimentAssignmentSubsets | List of Assignment subsets. |
| experimentCellSubsetChannelStatistics | Experiment cell subset channel statistics. |
| experimentCellSubsetCounts | Experiment cell subset counts. |
| experimentCellSubsetMap | Map experiment cell subsets to numerical values. |
| experimentDifferentialExpressionAnalysis | Differential expression analysis. |
| experimentLabelingStrategy | Experiment Assignment labeling strategy. |
| experimentMds | MDS map. |
| experimentSummary | Astrolabe experiment summary. |
| exportImmport | Immport export. |
| exportPlot | Export an orloj plot list. |
| exportReport | Export an orloj report. |
| fcsExprs | Get expression data from sample. |
| filenameify | Convert a string into a filename-friendly format. |
| findStandardMassCytometryChannels | Find indices of standard mass cytometry channels. |
| flowPreprocess | Preprocess flow cytometry sample. |
| formatPvalue | Format a p-value or FDR into a nice string. |
| getExperimentSampleFeatures | Get experiment sample features. |
| getSampleFilename | Get sample filename. |
| getSampleName | Get sample name. |
| identifyFcsInstrument | Identify FCS file instrument. |
| importCiteseqChannels | Import CITEseq Channel Information. |
| importFcsChannels | Import FCS Channel Information. |
| isFileCiteseq | Verify File is CITEseq. |
| isSample | Test if a given object is an Astrolabe sample. |
| jsDivergence | Jensen-Shannon Divergence |
| jsDivergenceMtx | Jensen-Shannon Divergence Between Matrices |
| kde2dVec | Vectorized Two-dimensional Kernel Density Estimation |
| loadExperiment | Load Astrolabe experiment. |
| loadSample | Load Astrolabe sample. |
| massPreprocess | Preprocess mass cytometry sample. |
| massTransformMassChannels | Transform expression data for mass cytometry sample. |
| nameVector | Name elements of vector with their value |
| plotBarPlot | Bar plot object. |
| plotBoxPlot | Box plot object. |
| plotHeatmap | Heat map object. |
| plotHeatmapAggregate | Aggregate data and generate a heat map object. |
| plotScatterPlot | Scatter plot object. |
| reportBeads | Bead report. |
| reportCellAssignments | Cell assignments report. |
| reportCellCounts | Cell counts report. |
| reportCombineAggregateStatistics | Combined aggregate statistics reports. |
| reportDifferentialAbundanceAnalysis | Differential abundance analysis report. |
| reportDifferentialExpressionAnalysis | Differential expression analysis report. |
| reportMarkerThresholds | Marker threshold report. |
| reportMds | MDS Map report. |
| reportNonCells | Non-cells report. |
| sampleCellSubsetChannelStatistics | Cell subset channel statistics. |
| sampleCellSubsetCounts | Cell subset counts. |
| sampleSummary | Astrolabe sample summary. |
