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

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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
ensureCountsFirst	Ensure counts assay is first
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
simPICMicrogliaExample	Run the Packaged Microglia splatPop Example
simPICplotBlusterComparison	Plot Poptrial-Style PCA, Silhouette, and Purity Comparisons
simPICplotPopulationPCA	Plot Population-Style PCA Summaries for Real Data
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
splatPopEstimatePeak	Estimate Peak-Based splatPop Parameters
splatPopSimulatePeak	Simulate Peak-Based Population Data with splatPop