# simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data

## Documentation for package ‘simPIC’ version 1.0.0

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

## 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
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 simPIC peak sparsity.
simPICget | Get a single simPICcount parameter
simPICgetparameters | Get parameters
simPICsimulate | simPIC simulation
simPICsimulateLibSize | Simulate simPIC library sizes
simPICsimulatePeakMean | Simulate simPIC peak means.
simPICsimulateTrueCounts | Simulate true counts.