splatter

DOI: 10.18129/B9.bioc.splatter    

This is the development version of splatter; for the stable release version, see splatter.

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Development (3.17)

Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.

Author: Luke Zappia [aut, cre] , Belinda Phipson [aut] , Christina Azodi [ctb] , Alicia Oshlack [aut]

Maintainer: Luke Zappia <luke at lazappi.id.au>

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("splatter")

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("splatter")

 

HTML	R Script	An introduction to the Splatter package
HTML	R Script	Splat simulation parameters
HTML	R Script	splatPop simulation
PDF		Reference Manual

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.23.0
In Bioconductor since	BioC 3.5 (R-3.4) (5.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 4.0), SingleCellExperiment
Imports	BiocGenerics, BiocParallel, checkmate (>= 2.0.0), edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods, scales, scater(>= 1.15.16), stats, SummarizedExperiment, utils, crayon, S4Vectors, grDevices
LinkingTo
Suggests	BiocStyle, covr, cowplot, magick, knitr, limSolve, lme4, progress, pscl, testthat, preprocessCore, rmarkdown, scDD, scran, mfa, phenopath, BASiCS(>= 1.7.10), zinbwave, SparseDC, BiocManager, spelling, igraph, scuttle, BiocSingular, VariantAnnotation, Biostrings, GenomeInfoDb, GenomicRanges, IRanges
SystemRequirements
Enhances
URL	https://github.com/Oshlack/splatter
BugReports	https://github.com/Oshlack/splatter/issues
Depends On Me
Imports Me	bcTSNE, SCRIP
Suggests Me	NewWave, scone, scPCA, SummarizedBenchmark
Links To Me
Build Report

Package Archives

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

Source Package	splatter_1.23.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/splatter
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/splatter
Package Short Url	https://bioconductor.org/packages/splatter/
Package Downloads Report	Download Stats