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Bioconductor - 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

Bioconductor version: Development (3.22)

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: 0000-0001-7744-8565 , GitHub: lazappi), Belinda Phipson [aut] (ORCID: ORCID: 0000-0002-1711-7454 , GitHub: bphipson), Christina Azodi [ctb] (ORCID: ORCID: 0000-0002-6097-606X , GitHub: azodichr), Alicia Oshlack [aut] 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 "4.5") 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")
Details biocViews GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics Version 1.33.1 In Bioconductor since BioC 3.5 (R-3.4) (8 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 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.

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