sismonr is an R package that I developed during my PhD for the simulation of gene expression profiles for in silico regulatory systems. Some innovative features of the model include:
- Simulation of protein-coding and noncoding genes
- Simulation of transcriptional and post-transcriptional regulation
- Simulation of the ploidy (number of gene copies) of the system
One originality of this package is that it relies on Julia code “under the hood” to speed up the computations. However, the user does not need to interact with Julia in order to use the package.
The package is publicly available on GitHub, and has been published in Bioinformatics. In addition, I developed together with NeSI a two-day workshop based on sismonr. I also had the chance to give a talk on sismonr at one of NESI’s webinars, the recording is available on Youtube.