Man pages for mkarikom/RSoptSC
Low-Rank Factorization for Subspace-clustering
| ApplyCountThreshold | Remove rare and ubiquitous genes |
| AvgFeatureExpression | Find average cluster feature expression |
| ClusterAvg | Create a heatmap with signaling markers over clusters |
| ClusterCells | Cluster the Cells |
| ClusterSig | Average cluster to cluster signaling. |
| ClusterSig_single | Average cluster to cluster signaling. |
| ColorHue | Get a vector of n equally spaced rgb colors |
| computeM | Perform ADMM |
| CountClusters | Use clustering consensus to infer cluster number |
| FeatureScatterPlot | Produce a scatter plot of the cells |
| FindRootCell | Find the root cell |
| FindRootCluster | Find the root cluster |
| getAlpha | compute lig and rec |
| getBetaj | compute uptargets |
| GetCellMetric | Get metric of pseudotime |
| GetComponents | Get graph components |
| GetConsensus | Produce a consensus matrix |
| GetCorrelation | Get rank correlation |
| GetDGFromTable | Get a weighted, directed graph from a table of edges and... |
| GetDominatorTree | Get a directed graph from a predecessor vector |
| GetEnsemble | Produce consensus matrix |
| getGammaj | compute downtargets |
| GetMarkerTable | Get the marker genes for each cluster |
| GetPredecessors | Get the predecessor vector for a dominator tree encoded as an... |
| GetSignalingPartners | Compute Cell-cell interaction probability |
| ImportPathway | Process siganling pathway data |
| JoinGraphComponents | Join Graph Components |
| LoadData | Load sequencing data and annotations |
| LogNormalize | Scale and center a data matrix |
| MembershipList | Get a list of membership vectors |
| PlotClusterExpression | Heatmap of specific genes |
| PlotLineage | Plot the pseudotime ordering of clusters |
| PlotMatlabDtree | Produce a plot of matlab DTree data and return the object |
| PlotTopN | Heatmap of the top n markers |
| PlotTopN_Grid | Factor Grid heatmap of the top n markers |
| ProcessMatlabDTree | Convert a matlab edge table and predecessor list into a... |
| RepresentationMap | Generate multiple representations |
| ScaleCenterData | Scale and center a data matrix |
| SelectData | Set of the most variable genes |
| SigPlot | Heatmap plot of cell signaling |
| SigPlot_Cluster | Heatmap plot of cluster signaling |
| SimilarityM | Compute the similarity matrix |
| SimpleCap | Capitalize the first letter of a string |
| updateFlatBoth | compute the unnormalized probability |
| updateFlatDown | compute the unnormalized probability |
| updateFlatNone | compute the unnormalized probability |
| updateFlatUp | compute the unnormalized probability |
| ViolinPlotExpression | Violin plot of gene expression |
