splatter

DOI: 10.18129/B9.bioc.splatter    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see splatter.

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: 3.9

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

Maintainer: Luke Zappia <luke.zappia at mcri.edu.au>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version	1.8.0
In Bioconductor since	BioC 3.5 (R-3.4) (2.5 years)
License	GPL-3 + file LICENSE
Depends	R (>= 3.4), SingleCellExperiment
Imports	akima, BiocGenerics, BiocParallel, checkmate, edgeR, fitdistrplus, ggplot2, locfit, matrixStats, methods, scales, scater(>= 1.7.4), stats, SummarizedExperiment, utils, crayon
LinkingTo
Suggests	BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager, spelling
SystemRequirements
Enhances
URL	https://github.com/Oshlack/splatter
BugReports	https://github.com/Oshlack/splatter/issues
Depends On Me
Imports Me
Suggests Me	SummarizedBenchmark
Links To Me
Build Report

Package Archives

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

Source Package	splatter_1.8.0.tar.gz
Windows Binary	splatter_1.8.0.zip
Mac OS X 10.11 (El Capitan)	splatter_1.8.0.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