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 (3.22)
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")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
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 | 1.5.3 |
| In Bioconductor since | BioC 3.19 (R-4.4) (1.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.5.0), SingleCellExperiment |
| Imports | BiocGenerics, checkmate (>= 2.0.0), fitdistrplus, matrixStats, actuar, Matrix, stats, SummarizedExperiment, rlang, S4Vectors, methods, scales, scuttle, edgeR, withr |
| System Requirements | |
| URL | https://github.com/sagrikachugh/simPIC |
| Bug Reports | https://github.com/sagrikachugh/simPIC/issues |
See More
| Suggests | ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0), scater, scran, magick |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simPIC_1.5.3.tar.gz |
| Windows Binary (x86_64) | simPIC_1.5.3.zip (64-bit only) |
| macOS Binary (x86_64) | simPIC_1.5.3.tgz |
| macOS Binary (arm64) | simPIC_1.5.3.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/ |
| Package Downloads Report | Download Stats |