simPIC

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see simPIC.

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

Bioconductor version: 3.19

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] , Davis McCarthy [aut], Heejung Shim [aut]

Maintainer: Sagrika Chugh <sagrika.chugh at gmail.com>

Citation (from within R, enter citation("simPIC")):

Installation

To install this package, start R (version "4.4") and enter:


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

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("simPIC")

simPIC: simulating single-cell ATAC-seq data HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software

Version 1.0.0

In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)

License GPL-3

Depends R (>= 4.4.0), SingleCellExperiment

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

System Requirements

URL https://github.com/sagrikachugh/simPIC

Bug Reports https://github.com/sagrikachugh/simPIC/issues

Suggests ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0)

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package simPIC_1.0.0.tar.gz

Windows Binary (x86_64) simPIC_1.0.0.zip (64-bit only)

macOS Binary (x86_64) simPIC_1.0.0.tgz

macOS Binary (arm64) simPIC_1.0.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/simPIC

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simPIC

Bioc Package Browser https://code.bioconductor.org/browse/simPIC/

Package Short Url https://bioconductor.org/packages/simPIC/

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