simPIC
This is the development version of simPIC; for the stable release version, see simPIC.
Flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
Bioconductor version: Development (3.24)
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("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.
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 | ||
| NEWS | Text |
Details
| biocViews | ATACSeq, DataImport, ImmunoOncology, Sequencing, SingleCell, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | GPL-3 |
| 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 |
| System Requirements | |
| URL | https://github.com/sagrikachugh/simPIC |
| Bug Reports | https://github.com/sagrikachugh/simPIC/issues |
See More
| Suggests | bluster, ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick, splatter, VariantAnnotation, IRanges, GenomicRanges, preprocessCore |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
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| Build Report | Build Report, r-universe |
Package Archives
Follow 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 (big-sur-x86_64) | simPIC_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | 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 Short Url | https://bioconductor.org/packages/simPIC/ |
| Package Downloads Report | Download Stats |