splatter

DOI: 10.18129/B9.bioc.splatter    

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Release (3.14)

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 "4.1") and enter:

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

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
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.18.2
In Bioconductor since	BioC 3.5 (R-3.4) (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, digitalDLSorteR, 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_1.18.2.tar.gz
Windows Binary	splatter_1.18.2.zip
macOS 10.13 (High Sierra)	splatter_1.18.2.tgz
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
Old Source Packages for BioC 3.14	Source Archive