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splatter (development version)

splatter

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

Simple Simulation of Single-cell RNA Sequencing Data

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DOI: 10.18129/B9.bioc.splatter

Bioconductor version: Development (3.23)

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] (ORCID: ORCID iD ORCID: 0000-0001-7744-8565 , GitHub: lazappi), Belinda Phipson [aut] (ORCID: ORCID iD ORCID: 0000-0002-1711-7454 , GitHub: bphipson), Christina Azodi [ctb] (ORCID: ORCID iD ORCID: 0000-0002-6097-606X , GitHub: azodichr), Alicia Oshlack [aut] ORCID iD ORCID: 0000-0001-9788-5690

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

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

Installation

To install this package, start R (version "4.6") 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")

An introduction to the Splatter package HTML R Script

Splat simulation parameters HTML R Script

splatPop simulation 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 1.35.0

In Bioconductor since BioC 3.5 (R-3.4) (8.5 years)

License GPL-3 + file LICENSE

Depends R (>= 4.0), SingleCellExperiment

Imports BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, locfit, matrixStats, methods, rlang, S4Vectors, scuttle, stats, SummarizedExperiment, utils, withr

System Requirements

URL https://bioconductor.org/packages/splatter/ https://github.com/Oshlack/splatter http://oshlacklab.com/splatter/

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

See More

Suggests BASiCS(>= 1.7.10), BiocManager, BiocSingular, BiocStyle, Biostrings, covr, cowplot, GenomeInfoDb, GenomicRanges, ggplot2 (>= 3.4.0), igraph, IRanges, knitr, limSolve, lme4, magick, mfa, phenopath, preprocessCore, progress, pscl, rmarkdown, scales, scater(>= 1.15.16), scDD, scran, SparseDC, spelling, testthat, VariantAnnotation, zinbwave

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me anglemania, ccImpute, HVP, mastR, NewWave, scone, scPCA, smartid, scellpam

Links To Me

Build Report Build Report

Package Archives

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

Source Package splatter_1.35.0.tar.gz

Windows Binary (x86_64) splatter_1.35.0.zip

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

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

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

Package Downloads Report Download Stats