GSR: Simulator - interSIM

Basic Package Attributes
AttributeValue
Title interSIM
Short Description InterSIM: simulation tool for multiple integrative omic datasets. Comput. Methods Prog. Biomed
Long Description Generates three inter-related genomic datasets : methylation, gene expression and protein expression. Input: Number of samples, proportion of samples in the cluster groups, cluster mean shift parameter delta and a few other options. Output: Generation of three datasets, methylation, gene expression and protein expression with inter- and intra- correlations having cluster group information. Also, the true clustering clustering assignment to each subject is generated.
Keywords Integrative, Clustering, Simulation, Inter, Intra
Version 2.2.0
Project Started 2016
Last Release 2 years, 9 months ago
Homepagehttps://cran.r-project.org/web/packages/InterSIM/index.html
Citations Chalise P, Raghavan R, Fridley BL, InterSIM: Simulation tool for multiple integrative 'omic datasets'., Comput Methods Programs Biomed, 05-01-2016 [ Abstract, cited in PMC ]
GSR Certification

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Last evaluated04-12-2021 (9 days ago)
Detailed Attributes
Attribute CategoryAttribute
Target
Type of Simulated Data
Variations
Simulation Method
Input
Data Type
File format
Output
Data TypeMethylation, Gene Expression, Protein Expression,
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
LicenseGNU Public License,
GSR CertificationAccessibility, Documentation, Application,

The following 7 publications are selected examples of applications that used interSIM.

2021

Cantini L, Zakeri P, Hernandez C, Naldi A, Thieffry D, Remy E, Baudot A, Benchmarking joint multi-omics dimensionality reduction approaches for the study of cancer., Nat Commun, 01-05-2021 [Abstract]

Wen Y, Song X, Yan B, Yang X, Wu L, Leng D, He S, Bo X, Multi-dimensional data integration algorithm based on random walk with restart., BMC Bioinformatics, 02-27-2021 [Abstract]

2020

Li J, Lu Q, Wen Y, Multi-kernel linear mixed model with adaptive lasso for prediction analysis on high-dimensional multi-omics data., Bioinformatics, 03-01-2020 [Abstract]

Chalise P, Ni Y, Fridley BL, Network-based integrative clustering of multiple types of genomic data using non-negative matrix factorization., Comput Biol Med, 03-01-2020 [Abstract]

2019

Hadi Fanaee, Magne Thoresen, Performance evaluation of methods for integrative dimension reduction, Information Sciences, 08-02-2019 [Abstract]

Fanaee-T H, Thoresen M, Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization., Bioinformatics, 05-15-2019 [Abstract]

2017

Chalise P, Fridley BL, Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm., PLoS One, 05-01-2017 [Abstract]


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