Package: simPIC 1.9.0

Sagrika Chugh

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

simPIC is a package for simulating single-cell ATAC-seq count data. It provides a user-friendly, well documented interface for data simulation. Functions are provided for parameter estimation, realistic scATAC-seq data simulation, and comparing real and simulated datasets.

Authors:Sagrika Chugh [aut, cre], Heejung Shim [aut], Davis McCarthy [aut]

simPIC_1.9.0.tar.gz
simPIC_1.9.0.zip(r-4.7)simPIC_1.9.0.zip(r-4.6)simPIC_1.9.0.zip(r-4.5)
simPIC_1.9.0.tgz(r-4.6-any)simPIC_1.9.0.tgz(r-4.5-any)
simPIC_1.9.0.tar.gz(r-4.7-any)simPIC_1.9.0.tar.gz(r-4.6-any)
simPIC_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simPIC/json (API)

# Install 'simPIC' in R:
install.packages('simPIC', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sagrikachugh/simpic/issues

On BioConductor:simPIC-1.9.0(bioc 3.24)simPIC-1.8.0(bioc 3.23)

singlecellatacseqsoftwaresequencingimmunooncologydataimportbioconductorbioinformaticsscatac-seqsimulation

4.00 score 10 scripts 14 exports 62 dependencies

Last updated from:9c476fcc17. Checks:1 WARNING, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING225
linux-devel-x86_64OK386
source / vignettesOK331
linux-release-x86_64OK395
macos-release-arm64OK288
macos-oldrel-arm64OK251
windows-develOK410
windows-releaseOK308
windows-oldrelOK328
wasm-releaseOK204

Exports:newsimPICcountsetsimPICparameterssimPICcomparesimPICestimatesimPICgetsimPICgetparameterssimPICMicrogliaExamplesimPICplotBlusterComparisonsimPICplotPopulationPCAsimPICsimulatesimPICsimulatemultisimPICsimulatesinglesplatPopEstimatePeaksplatPopSimulatePeak

Dependencies:abindactuaraskpassassortheadbackportsbeachmatBHBiobaseBiocGenericsBiocParallelcheckmateclicodetoolscpp11curlDelayedArrayedgeRexpintfarverfitdistrplusformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicRangesgluehttrIRangesjsonlitelabelinglambda.rlatticelifecyclelimmalocfitMASSMatrixMatrixGenericsmatrixStatsmimeopensslR6RColorBrewerRcpprlangS4ArraysS4VectorsscalesscuttleSeqinfoSingleCellExperimentsnowSparseArraystatmodSummarizedExperimentsurvivalsysUCSC.utilsviridisLitewithrXVector

simPIC Microglia Population Example
Overview | Packaged example data | Quick Start | Quick-Start Plots | Detailed Look | Why bigcounts? | Plotting Subset | Interpreting The Plots | Notes | Session information
Rendered fromvignette_population.Rmdusingknitr::rmarkdown

Last update: 2026-05-28
Started: 2026-05-27

simPIC: simulating single-cell ATAC-seq data
Introduction | Installation | Quick start | Input data | simPIC simulation | simPICcount class | Getting and setting parameters | Estimating Parameters | Simulating counts | Comparing Simulations and Real Data | Simulating Multiple Cell Types - equal proportions | Simulating Multiple Cell Types - variable proportions | Simulating Batch effects | Citing simPIC | Session information
Rendered fromvignette.Rmdusingknitr::rmarkdown

Last update: 2026-05-27
Started: 2024-02-28

Readme and manuals

Help Manual

Help pageTopics
Add feature statisticsaddFeatureStats
Convert Sparse Matrix to SingleCellExperiment objectconvert_to_SCE
Ensure counts assay is firstensureCountsFirst
Get counts from Single Cell Experiment objectgetCounts
simPIC: Simulate single-cell ATAC-seq dataglobal
newsimPICcountnewsimPICcount
Custom theme for ggplot2plot_theme
Bind rows (matched)rbindMatched
Select fitselectFit
Set simPIC parameterssetsimPICparameters
Compare SingleCellExperiment objectssimPICcompare
The simPICcount classsimPICcount simPICcount-class
Estimate simPIC Biological Coefficient of Variation parameterssimPICEstBCV
Estimate simPIC simulation parameterssimPICestimate simPICestimate.dgCMatrix simPICestimate.SingleCellExperiment
Estimate simPIC library size parameterssimPICestimateLibSize
Estimate simPIC peak meanssimPICestimatePeakMean
Estimate sparsitysimPICestimateSparsity
Get a single simPICcount parametersimPICget
Get parameterssimPICgetparameters
Run the Packaged Microglia splatPop ExamplesimPICMicrogliaExample
Plot Poptrial-Style PCA, Silhouette, and Purity ComparisonssimPICplotBlusterComparison
Plot Population-Style PCA Summaries for Real DatasimPICplotPopulationPCA
Simulate cell meanssimPICsimCellMeans simPICsimSingleCellMeans simPICsimulateGroupCellMeans
simPIC simulationsimPICsimulate simPICsimulatemulti simPICsimulatesingle
Simulate BCV meanssimPICsimulateBCVMeans
Simulate simPIC library sizessimPICsimulateLibSize
Simulate group differential accessibilitysimPICsimulatemultiDA
Simulate simPIC peak meanssimPICsimulatePeakMean
Simulate true countssimPICsimulateTrueCounts
Simulate true counts groupssimPICsimulateTrueCountsGroups
Estimate Peak-Based splatPop ParameterssplatPopEstimatePeak
Simulate Peak-Based Population Data with splatPopsplatPopSimulatePeak