# MOSim MOSim is an R package for the simulation of multi-omic bulk and single cell experiments that mimic regulatory mechanisms within the cell. Gene expression (RNA-seq count data) is the central data type simulated by MOSim, while the rest of available omic data types provide gene regulation information. For bulk simulation, regulators include ATAC-seq (DNase-seq), ChIP-seq, miRNA-seq and Methyl-seq. In addition to these omics, regulation by transcription factors (TFs) can also be modeled. While for single-cell simulation, the regulators included are scATAC-seq and TFs. ### Installation MOSim is a Bioconductor R package, and we strongly recommend that it is installed from the Bioconductor repository. To install MOSim, open the R console and run: ``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("MOSim") ``` The developer version (which now includes the sc_mosim functionalities) can be installed from GitHub using the devtools R package: ``` install.packages("devtools") devtools::install_github("ConesaLab/MOSim") ``` ### Documentation Vignettes and documentation can be accessed from [MOSim's Bioconductor site](http://bioconductor.org/packages/release/bioc/html/MOSim.html), or by running the following line in the R console: browseVignettes("MOSim") ### Citation If you used MOSim for your research, please cite: - Monzó C, Martínez C, Arzalluz-Luque A, Conesa A, Tarazona S (2024). MOSim: bulk and single-cell multi-layer regulatory network simulator. BioRxiv. DOI: 10.1101/421834 sc_mosim strongly relies on functionality from SPARSim. If you use the sc_mosim module to simulate multi-omics single cell data, please also cite: - Baruzzo G, Patuzzi I, Di Camillo B (2020). SPARSim single cell: a count data simulator for scRNA-seq data. Bioinformatics, Volume 36, Issue 5, Pages 1468-1475. DOI: 10.1093/bioinformatics/btz752