simPIC
This is the development version of simPIC; for the stable release version, see simPIC.
All Bioconductor versions of simPIC
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
Bioconductor version: 3.24 · Package version: 1.9.0
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.
Author: Sagrika Chugh [aut, cre] 
, Heejung Shim [aut], Davis McCarthy [aut]
Maintainer: Sagrika Chugh <sagrika.chugh at gmail.com>
Citation
From within R, enter citation("simPIC"):
Sagrika Chugh, Heejung Shim, Davis McCarthy. simPIC: Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data. doi:10.18129/B9.bioc.simPIC, R package version 1.9.0, https://bioconductor.org/packages/simPIC.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("simPIC")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.9.0 |
| License | GPL-3 |
| URL | https://github.com/sagrikachugh/simPIC |
| Bug Reports | https://github.com/sagrikachugh/simPIC/issues |
| Last updated | 2026-05-28 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2 years) |
| Downloads rank | 1724 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/simPIC/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simPIC")| simPIC Microglia Population Example | HTML | |
| simPIC: simulating single-cell ATAC-seq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | simPIC_1.9.0.tar.gz |
| Windows binary (x86_64) | simPIC_1.9.0.zip |
| macOS binary (arm64) | simPIC_1.9.0.tgz |
| macOS binary (x86_64) | simPIC_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/simPIC |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/simPIC |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.5.0), SingleCellExperiment
Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, GenomeInfoDb, methods, scales, scuttle, edgeR, withr
Suggests: bluster, ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick, splatter, VariantAnnotation, IRanges, GenomicRanges, preprocessCore