simPIC

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

Bioconductor version: 3.23 · Package version: 1.8.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simPIC")

Details

Maintainer	Sagrika Chugh <sagrika.chugh@gmail.com>
Author	Sagrika Chugh [aut, cre] (ORCID: <https://orcid.org/0000-0002-8050-5214>), Heejung Shim [aut], Davis McCarthy [aut]
License	GPL-3
URL	https://github.com/sagrikachugh/simPIC
Bug Reports	https://github.com/sagrikachugh/simPIC/issues
Downloads rank	182
Source branch	RELEASE_3_23
biocViews	ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software

Documentation

simPIC: simulating single-cell ATAC-seq data

Download

Source package

Dependencies

Depends: R (>= 4.5.0), SingleCellExperiment

Imports: BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr

Suggests: ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick