# Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data

## Documentation for package ‘simPIC’ version 1.9.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

addFeatureStats | Add feature statistics
convert_to_SCE | Convert Sparse Matrix to SingleCellExperiment object
getCounts | Get counts from Single Cell Experiment object
global | simPIC: Simulate single-cell ATAC-seq data
newsimPICcount | newsimPICcount
plot_theme | Custom theme for ggplot2
rbindMatched | Bind rows (matched)
selectFit | Select fit
setsimPICparameters | Set simPIC parameters
simPICcompare | Compare SingleCellExperiment objects
simPICcount | The simPICcount class
simPICcount-class | The simPICcount class
simPICEstBCV | Estimate simPIC Biological Coefficient of Variation parameters
simPICestimate | Estimate simPIC simulation parameters
simPICestimate.dgCMatrix | Estimate simPIC simulation parameters
simPICestimate.SingleCellExperiment | Estimate simPIC simulation parameters
simPICestimateLibSize | Estimate simPIC library size parameters.
simPICestimatePeakMean | Estimate simPIC peak means
simPICestimateSparsity | Estimate sparsity.
simPICget | Get a single simPICcount parameter
simPICgetparameters | Get parameters
simPICsimCellMeans | Simulate cell means
simPICsimSingleCellMeans | Simulate cell means
simPICsimulate | simPIC simulation
simPICsimulateBCVMeans | Simulate BCV means
simPICsimulateGroupCellMeans | Simulate cell means
simPICsimulateLibSize | Simulate simPIC library sizes
simPICsimulatemulti | simPIC simulation
simPICsimulatemultiDA | Simulate group differential accessibility
simPICsimulatePeakMean | Simulate simPIC peak means.
simPICsimulatesingle | simPIC simulation
simPICsimulateTrueCounts | Simulate true counts.
simPICsimulateTrueCountsGroups | Simulate true counts groups.