Man pages for PFPrzytycki/CellWalkR
An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements
| clusterLabels | Cluster labels |
| combineGraph | Generate combined graph |
| combineMultiLabelGraph | Generate combined graph with list of label edges |
| computeCellHomogeneity | Compute cell homogeneity |
| computeCellSim | Compute Cell Similarity |
| computeLabelEdges | Compute Label Edges |
| computeMST | Comptute Minimum Spanning Tree |
| downloadSampleData | Download Sample Data |
| findMarkers | Find markers in scRNA-seq data |
| findUncertainLabels | Find uncertain labels |
| getRegions | Get genomic regions |
| labelBulk | Label bulk data |
| launchViz | Launch Interactve Visualization |
| loadSampleData | Load Sample Data |
| mapArchRToGenes | Map ArchR peaks to genes |
| mapCiceroToGenes | Map peaks to genes based on Cicero coaccessibility |
| mapPeaksToGenes | Map peaks to genes |
| mapSnapATACToGenes | Map SnapATAC peaks to genes |
| normalizeInfluence | Normalize influence matrix |
| PCAdist | Compute distance in PCA space for matrix |
| plotCells | Plot Cells |
| plotMultiLevelLabels | Plot significant labels across heirarchy |
| randomWalk | Random walk with restarts |
| SampleCellWalkRData | List of 10 items used to test CellWalkR |
| scoreDoublets | Score doublets |
| selectLabels | Select significant labels |
| selectMultiLevelLabels | Select significant labels across heirarchy |
| sparseJaccard | Compute Jaccard on sprase matrix |
| storeBulk | Store bulk label data |
| storeMat | Store ATACMat data |
| tensorJaccard | Compute Jaccard on matrix using tensorflow |
| tuneEdgeWeights | Tune edge weights |
| tuneFilterWeights | Tune filter weights |
| walkCells | Run CellWalker Method |
