Package index • sCCIgen

All functions

Add.Distance.Asso.Pattern(): Add cell-cell expr-distance interaction to a pair of cell types

Add.Expr.Asso.Pattern(): Add cell-cell expr-expr interaction pattern to a pair of cell types

Add.Spatial.Expr.Pattern(): Adds spatial differential expressed pattern (region-specific effects) to a cell type.

Est_ModelPara(): Estimate Marginal distribution and Gaussian Copula for Gene Expression Matrix

ExprDistanceTable(): Save cell expression - distance patterns for simulation

ExprExprTable(): Save cell expression - cell expression association patterns for simulation

MergeRegion(): Merge spatial and expression data from multiple regions

ParaCellsNoST(): Use parameters to simulate cell location (no existing spatial info)

ParaCellsST(): Use parameters to simulate cell location based on modeling of existing SRT

ParaDigest(): Digest the parameter file.

ParaExistingCellsST(): Use parameters to simulate cell location (direct output from existing spatial data)

ParaExpr(): Simualte gene expression data based on parameters

ParaSimulation(): (Main Function) Simulate spatially resolved transcriptomics data from a parameter file.

Pattern.Adj(): Adjust the count data for all cells in all regions based on the input spatial patterns

RandomRegionWindow(): Generate random connected region in a window

SpatialTable(): SpatialTable

Use_scDesign2(): Generate expression profile under no spatial patterns.

cell.loc.existing.fc(): Generate cell location data by using existing SRT data directly.

cell.loc.fc(): Generate cell location data from parameters.

cell.loc.model.fc(): Generate cell location data by modeling the spatial information of existing data.

cellProximityTable(): Save cell attraction and inhibition patterns for simulation

connectUp(): Assign connected regions in a window

df_to_config(): Convert a data.frame to config.yml

fit_Gaussian_copula(): Fit a Gaussian copula model for a count matrix of a single cell type

fit_model_scDesign2(): Fit models for a count matrix

fit_wo_copula(): Fit a (w/o copula) model for a count matrix of a single cell type

loadRData(): load RData with new assigned file name

multicell(): Assigns cells into spatial spots for multi-cell resolution data

preprocessGiotto(): Process SRT data using Giotto for CCI analysis.

run_interactive_sCCIgen(): Run interactive sCCIgen

sCCIgen_to_Giotto(): Convert sCCIgen output to a Giotto object

sCCIgen_to_Seurat(): Convert sCCIgen output to a Seurat object

sCCIgen_to_SpatialExperiment(): Convert sCCIgen output to a SpatialExperiment object

scDesign2.revised(): Simulate a count matrix for a single cell type

simu.window(): Simulate the window of spatial data

simulate_count_copula(): Simulate a count matrix for a single cell type based on a copula model

simulate_count_ind(): Simulate a count matrix for a single cell type based on a (w/o copula model)