simPIC
simPIC: flexible simulation of paired-insertion counts for single-cell ATAC-sequencing data
Bioconductor version: Release (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("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 | ||
NEWS | Text |
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 |
See More
Suggests | ggplot2 (>= 3.4.0), knitr, rmarkdown, BiocStyle, testthat (>= 3.0.0) |
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_1.0.0.tar.gz |
Windows Binary | 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/ |
Package Downloads Report | Download Stats |