Package index • compact

All functions

AlertHeatmap(): AlertHeatmap: visualize pathway-level perturbation metrics as a heatmap
AlertSystemScore(): AlertSystem: score pathway gene sets for a given module perturbation
ApplyPerturbation(): Apply In-Silico Perturbation
ApplyPropagation(): Propagate In-Silico Perturbation Signal Through a Gene Network
BarplotShap(): Plot Bar Chart of Top SHAP Driver Genes
BeeswarmplotShap(): Plot SHAP Beeswarm Summary for Top Driver Genes
CheckSaturation(): Check for Signal Saturation After Network Propagation
CheckSignalDecay(): Check for Propagation Signal Decay
CombinePerturbAssays(): CombinePerturbAssays: create a composite perturb assay by delta superposition (sparse-safe; COUNTS-only)
ComputeDistance(): ComputeDistance
CustomPerturbation(): CustomPerturbation
FindConnectedComponents(): FindConnectedComponents
FindShapKeyDriver(): Identify Key Driver Genes Using SHAP and XGBoost
HeatmapDistance(): HeatmapDistance: Generate Heatmaps for Original and Perturbed Matrices
LoadAlertSystem(): Load a previously saved AlertSystem state into a Seurat object
LoadAlertSystemPathways(): Load AlertSystem pathway gene sets (local or GitHub)
MacrostateTransitions(): MacrostateTransitions
ModelZINB(): ModelZINB
ModulePerturbation(): ModulePerturbation
PerturbationLog2FC(): Calculate Log2 Fold Change of In-Silico Perturbation
PerturbationTransitions(): PerturbationTransitions
PerturbationVectors(): Calculate Perturbation Transition Vectors for Cell Embeddings
PlotMacrostateTransitions(): PlotMacrostateTransitions
PlotTransitionVectors(): Plot Transition Vectors on a Reduced Dimensional Embedding
PredictAttractors(): Predict Perturbation Attractor States
PredictCommitment(): Predict Fate Commitment (Committor Probabilities)
PredictFates(): Predict Perturbation Fates (Forward Diffusion)
PredictPerturbationTime(): Predict Perturbation Pseudotime (Absorbing Markov Chain Hitting Time)
ReloadShapOutput(): Reload SHAP Output from Disk
SampleZINB(): SampleZINB
SaveAlertSystem(): Save the full AlertSystem state to disk
StampPerturbProvenance(): StampPerturbProvenance: record baseline provenance for a perturb assay
TFPerturbation(): TFPerturbation
VectorFieldCoherence(): Compute Local Coherence of a Vector Field
.create_distance_heatmap(): This function generates a heatmap from a given matrix. It handles both matrices and data frames (converting them to matrices if needed). It also allows customization of the color palette, axis visibility, and legend display.
.edist(): edist
.eucldist(): eucldist
.get_upper_tri(): This function is used internally to extract the upper triangle of a matrix. It replaces the lower triangle of the input matrix with NA, which is useful when working with symmetrical matrices such as distance or correlation matrices where only the upper triangle is needed.
.spearmandist(): spearmandist