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>

Citation (from within R, enter citation("splatter")):

Installation

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

An introduction to the Splatter package HTML R Script

Splat simulation parameters HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics

Version 1.8.0

In Bioconductor since BioC 3.5 (R-3.4) (7 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

System Requirements

URL https://github.com/Oshlack/splatter

Bug Reports https://github.com/Oshlack/splatter/issues

Suggests BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager, spelling

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me SummarizedBenchmark

Links To Me

Build Report 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

Bioc Package Browser https://code.bioconductor.org/browse/splatter/

Package Short Url https://bioconductor.org/packages/splatter/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.9 Source Archive