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 (3.21)
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] (ORCID:
Maintainer: Hechen Li <hli691 at gatech.edu>
citation("scMultiSim")):
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("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 | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | scMultiSim_1.3.0.zip (64-bit only) |
| macOS Binary (x86_64) | scMultiSim_1.3.0.tgz |
| macOS Binary (arm64) | |
| 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 |