Package index • SecAct

Core Functions

Primary functions for activity inference

SecAct.inference.gsl(): Secreted protein activity inference

SecAct.inference.r(): Secreted protein activity inference

SecAct.activity.inference(): Secreted protein activity inference

Data Type Specific

Functions for different data types

SecAct.activity.inference.ST(): Spot activity inference from spatial data

SecAct.activity.inference.scRNAseq(): Cell state activity inference from single cell data

Downstream Analysis

Cell-cell communication and pattern analysis

SecAct.signaling.pattern(): Secreted protein signaling pattern

SecAct.signaling.pattern.gene(): Pattern-associated secreted proteins

SecAct.signaling.velocity.spotST(): Secreted protein signaling velocity

SecAct.signaling.velocity.scST(): Secreted protein signaling velocity for single-cell ST

SecAct.CCC.scST(): Cell-cell communication from spatial data

SecAct.CCC.scRNAseq(): Cell-cell communication from single cell data

SecAct.coxph.regression(): Survival regression

Visualization

Plotting functions

SecAct.heatmap.plot(): Draw a heatmap plot

SecAct.bar.plot(): Draw a bar plot

SecAct.lollipop.plot(): Draw a lollipop plot

SecAct.survival.plot(): Draw a survival plot

SecAct.CCC.heatmap(): Cell-cell communication heatmap

SecAct.CCC.circle(): Cell-cell communication circle plot

SecAct.CCC.sankey(): Cell-cell communication sankey plot

SecAct.CCC.dot(): Cell-cell communication dot plot