splatter

DOI: 10.18129/B9.bioc.splatter    

This is the development version of splatter; to use it, please install the devel version of Bioconductor.

Simple Simulation of Single-cell RNA Sequencing Data

Bioconductor version: Development (3.10)

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

Details

biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics
Version 1.9.3
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(>= 1.13.11), stats, SummarizedExperiment, utils, crayon, S4Vectors
LinkingTo
Suggests BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, 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_1.9.3.tar.gz
Windows Binary splatter_1.9.3.zip
Mac OS X 10.11 (El Capitan) splatter_1.9.3.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 http://bioconductor.org/packages/splatter/
Package Downloads Report Download Stats

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