neurergus / mosim

Multi-Omics Simulation in R

IMPORTANT: This software is now hosted in the ConesaLab github: https://github.com/ConesaLab/MOSim

For the latest version of the software as well as issues and questions, please head to the new site.

MOSim

MOSim is an R package for the simulation of multi-omic 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 and include ATAC-seq (DNase-seq), ChIP-seq, small RNA-seq and Methyl-seq. In addition to these omics, regulation by transcription factors (TFs) can also be modeled.

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 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, or by running the following line in the R console:

browseVignettes("MOSim")

Citation

If you used MOSim for your research, please cite:

• Martínez C, Monzó C, Conesa A, Tarazona S (2022). MOSim: Multi-Omics Simulation (MOSim). R package version 1.2.0, https://github.com/ConesaLab/MOSim.

mosim's Issues

Simulate with existing data

Hi,
Nice package for multi-omics! Many thanks for developing and maintaining it.

I have a multi-omic dataset and wanted to create a simulated dataset based on it.
That dataset have a block of data coming from 16S sequencing. Is there any way to simulate it with MOSim?
I would have expected that providing my own data to base the synthetic dataset could work but then I read that they must be from the accepted data types, and I only see these:

• RNA-seq (compulsory)
• DNase-seq
• ChIP-seq
• Methyl-seq
• miRNA-seq

Also I'm not familiar enough with the code base, how are the provided datasets used for the simulation?

Many thanks