Landscape Expression Visualization and Network Inference
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Documentation for package ‘levi’ version 1.99.0
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| bimodal_dataset | Bimodal toy dataset |
| bimodal_expression | Bimodal toy dataset |
| bimodal_network | Bimodal toy dataset |
| flat_dataset | Flat (null-expression) toy dataset |
| flat_expression | Flat (null-expression) toy dataset |
| flat_network | Flat (null-expression) toy dataset |
| gradient_dataset | Gradient-topology toy dataset |
| gradient_expression | Gradient-topology toy dataset |
| gradient_network | Gradient-topology toy dataset |
| hub_dataset | Hub-topology toy dataset |
| hub_expression | Hub-topology toy dataset |
| hub_multicomp_expression | Multi-comparison toy dataset |
| hub_network | Hub-topology toy dataset |
| levi | levi |
| leviAdjustPathways | Adjust regional LEVI results across pathways or networks |
| leviBulkGraphInference | Bulk RNA-seq graph-cluster inference |
| leviDiff | leviDiff |
| leviEnrich | leviEnrich |
| leviFromBioc | leviFromBioc |
| leviFromDESeq2 | leviFromDESeq2 |
| leviFromEdgeR | leviFromEdgeR |
| leviFromEdges | leviFromEdges |
| leviFromExpressionSet | leviFromExpressionSet |
| leviFromLimma | leviFromLimma |
| leviFromSE | leviFromSE |
| leviFromSeurat | leviFromSeurat |
| leviFromSTRING | leviFromSTRING |
| leviGraphClusterInference | Graph-connected cluster-mass inference from biological replicates |
| leviGraphGetisOrd | Getis-Ord hotspots and coldspots on a biological graph |
| leviGraphMoran | Moran global and local autocorrelation on a biological graph |
| leviGraphRewiringInference | Degree-preserving rewiring test for graph clusters |
| leviGraphSpectrum | Laplacian smoothness and graph-Fourier low-frequency energy |
| leviGraphTFCEFreedmanLane | Graph TFCE with Freedman-Lane residual permutation |
| leviGraphTFCEInference | Threshold-free graph-cluster enhancement with sample-label inference |
| leviGraphTFCERewiring | Degree-preserving rewiring sensitivity test for graph TFCE |
| leviGraphWeightedTopology | Weighted Moran and Laplacian statistics for scored biological interactions |
| leviGrid | leviGrid |
| leviPseudobulk | Aggregate single-cell counts to pseudobulks |
| leviRegionGenes | Attribute a LEVI region to nearby network genes |
| leviReplicateInference | Regional inference from biological replicates |
| leviSave3D | Save the 3D landscape surface from a chosen viewpoint |
| leviSingleCellGraphInference | Single-cell pseudobulk graph-cluster inference |
| leviSingleCellInteractionTFCE | Cell-type-specific condition interaction with joint graph TFCE inference |
| leviSingleCellRegionalInference | Joint regional inference for paired single-cell pseudobulks |
| leviSingleCellTFCEInference | Cell-type-specific TFCE inference for pseudobulk single-cell RNA-seq |
| leviSingleCellTopologyInference | Run Moran, Laplacian/Fourier and rewiring tests per cell type |
| LEVIui | LEVIui - Interactive Shiny GUI for levi |
| logfc_dataset | Log2-intensity (logfc-mode) toy dataset |
| logfc_expression | Log2-intensity (logfc-mode) toy dataset |
| logfc_network | Log2-intensity (logfc-mode) toy dataset |
| multicomp_dataset | Multi-comparison toy dataset |
| print.levi_result | Print a levi result |
| readExpColumn | readExpColumn - Define expression comparisons for levi |
| sparse_dataset | Sparse-expression toy dataset |
| sparse_expression | Sparse-expression toy dataset |
| sparse_network | Sparse-expression toy dataset |