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Bioconductor - simPIC

simPIC

This is the released version of simPIC; for the devel version, see simPIC.

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

Bioconductor version: Release (3.21)

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] ORCID: 0000-0002-8050-5214 , 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 "4.5") 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")
Details biocViews ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software Version 1.4.0 In Bioconductor since BioC 3.19 (R-4.4) (1 year) 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 See More Package Archives

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

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