GSR: Simulator - OmicsSIMLA

Basic Package Attributes
AttributeValue
Title 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.
Version 0.6
Project Started 2019
Homepage
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 verificationThe 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.
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated DataHaploid DNA Sequence, Protein Sequence,
VariationsBiallelic Marker, Other,
Simulation Method
Input
Data TypeReference genome,
File format
Output
Data Type
Sequencing Reads
File Format
Sample Type
Phenotype
Trait Type
Determinants
Evolutionary Features
Demographic
Population Size Changes
Gene Flow
Spatiality
Life Cycle
Mating System
Fecundity
Natural Selection
Determinant
Models
Recombination
Mutation Models
Events Allowed
Other
Interface
Development
Tested Platforms
LanguageC or C++, R,
License
GSR Certification

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