splatter
Simple Simulation of Single-cell RNA Sequencing Data
Bioconductor version: 3.23 · Package version: 1.36.0
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("splatter")Details
| Maintainer | Luke Zappia <luke@lazappi.id.au> |
| Author | Luke Zappia [aut, cre] (ORCID: <https://orcid.org/0000-0001-7744-8565>, GitHub: lazappi), Belinda Phipson [aut] (ORCID: <https://orcid.org/0000-0002-1711-7454>, GitHub: bphipson), Christina Azodi [ctb] (ORCID: <https://orcid.org/0000-0002-6097-606X>, GitHub: azodichr), Alicia Oshlack [aut] (ORCID: <https://orcid.org/0000-0001-9788-5690>) |
| License | GPL-3 + file LICENSE |
| URL | https://bioconductor.org/packages/splatter/, https://github.com/Oshlack/splatter, http://oshlacklab.com/splatter/ |
| Bug Reports | https://github.com/Oshlack/splatter/issues |
| Downloads rank | 842 |
| Source branch | RELEASE_3_23 |
| biocViews | GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcriptomics |
Documentation
- Introduction to Splatter
- Splat simulation parameters
- splatPop: simulating single-cell data for populations
Download
Dependencies
Depends: R (>= 4.0), SingleCellExperiment
Imports: BiocGenerics, BiocParallel, checkmate (>= 2.0.0), crayon, edgeR, fitdistrplus, grDevices, lifecycle, locfit, matrixStats, methods, rlang, S4Vectors, scrapper, scuttle, stats, SummarizedExperiment, utils, withr
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