GSR: Simulator - OmicsSIMLA
Attribute | Value |
---|---|
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 | Accessibility |
Last evaluated | 09-30-2021 (926 days ago) |
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. |
Attribute Category | Attribute |
---|---|
Target | |
Type of Simulated Data | Haploid DNA Sequence, Protein Sequence, |
Variations | Biallelic Marker, Other, |
Simulation Method | |
Input | |
Data Type | Reference 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 | |
Language | C or C++, R, |
License | |
GSR Certification | Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 2
The following 2 publications are selected examples of applications that used OmicsSIMLA.
2023
Snajder R, Leger A, Stegle O, Bonder MJ, pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls., Genome Biol, 04-20-2023 [Abstract]
2022
Pierre-Jean M, Mauger F, Deleuze JF, Le Floch E, PIntMF: Penalized Integrative Matrix Factorization method for multi-omics data., Bioinformatics, 01-27-2022 [Abstract]