GSR: Simulator - OmicsSIMLA
|Short Description||A simulation tool for generating multi-omics data with disease status|
|Long Description||OmicsSIMLA is a simulation tool for generating multi-omics data with disease status. Currently, OmicsSIMLA has four main modules: SeqSIMLA, pWGBSSimla, RNA-Seq, and RPPA. SeqSIMLA can simulate sequence data in families with multiple affected and unaffected siblings or unrelated case-control samples under different disease models. pWGBSSimla is a profile-based whole-genome bisulphite sequencing data simulator, which can simulate whole-genome DNA methylation (WGBS), reduced representation bisulfite sequencing (RRBS), and oxidative bisulfite sequencing (oxBS-seq) data while modeling methylation quantitative trait loci, allele-specific methylations, and differentially methylated regions. RNA-Seq uses a negative binomial distribution to simulate NGS read counts for gene expression. Finally, RPPA uses a mass-action kinetic action model to simulate protein expression data.|
|Citations||Chung RH, Kang CY, A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification., Gigascience, 05-01-2019 [ Abstract, cited in PMC ]|
|GSR Certification||This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification.|
|Author verification||The basic description provided was derived from a website or publications by the GSR team and has not yet been verified by the simulation author. To modify this entry or add more information, propose changes to this simulator.|
|Type of Simulated Data||Haploid DNA Sequence, Protein Sequence,|
|Variations||Biallelic Marker, Other,|
|Data Type||Reference genome,|
|Population Size Changes|
|Language||C or C++, R,|
No example publication using OmicsSIMLA has been provided.
Please propose new citations if you are aware of publications that use this software.