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

DiffLimits(): Shared colour limits across several difference matrices

FindConnectedComponents(): FindConnectedComponents

FindShapKeyDriver(): Identify Key Driver Genes Using SHAP and XGBoost

HeatmapDistance(): HeatmapDistance: Generate Heatmaps for Original and Perturbed Matrices

HeatmapDistanceDiff(): Diverging heatmap of a difference matrix (post - pre)

HeatmapDistanceTriptych(): Pre / post / difference triptych

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

PlotMarkovEmbedding(): Plot a Markov Score on a Dimensionality Reduction Embedding

PlotMarkovScatter(): Scatter Plot of Two Markov or Biological Features

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)

ProjectPCAReference(): Project an assay into an existing PCA reference space

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

TargetModulePerturbation(): Perturb one co-expression module in a selected population only

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