scMultiSim
This is the development version of scMultiSim; for the stable release version, see scMultiSim.
Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell Interactions
Bioconductor version: Development (3.24)
scMultiSim simulates paired single cell RNA-seq, single cell ATAC-seq and RNA velocity data, while incorporating mechanisms of gene regulatory networks, chromatin accessibility and cell-cell interactions. It allows users to tune various parameters controlling the amount of each biological factor, variation of gene-expression levels, the influence of chromatin accessibility on RNA sequence data, and so on. It can be used to benchmark various computational methods for single cell multi-omics data, and to assist in experimental design of wet-lab experiments.
Author: Hechen Li [aut, cre]
, Xiuwei Zhang [aut], Ziqi Zhang [aut], Michael Squires [aut]
Maintainer: Hechen Li <hli691 at gatech.edu>
citation("scMultiSim")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("scMultiSim")
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("scMultiSim")| 1. Getting Started | HTML | R Script |
| 2. Simulating Multimodal Single-cell Datasets | HTML | R Script |
| 3. Simulating Spatial Cell-Cell Interactions | HTML | R Script |
| 4. Parameter Guide | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | ExperimentalDesign, GeneExpression, Sequencing, SingleCell, Software, Transcriptomics |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.4.0) |
| Imports | foreach, rlang, dplyr, ggplot2, Rtsne, ape, MASS, matrixStats, phytools, KernelKnn, gplots, zeallot, crayon, assertthat, igraph, methods, grDevices, graphics, stats, utils, markdown, SummarizedExperiment, BiocParallel |
| System Requirements | |
| URL | https://zhanglabgt.github.io/scMultiSim/ |
| Bug Reports | https://github.com/ZhangLabGT/scMultiSim/issues |
See More
| Suggests | knitr, rmarkdown, roxygen2, shiny, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | scMultiSim_1.9.0.tar.gz |
| Windows Binary (x86_64) | scMultiSim_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | scMultiSim_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | scMultiSim_1.9.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/scMultiSim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/scMultiSim |
| Bioc Package Browser | https://code.bioconductor.org/browse/scMultiSim/ |
| Package Short Url | https://bioconductor.org/packages/scMultiSim/ |
| Package Downloads Report | Download Stats |