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GSR: Simulator - interSIM
| Attribute | Value |
|---|---|
| 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 | 7 years, 3 months ago |
| Homepage | https://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, May 1, 2016 [ Abstract, cited in PMC ] |
| GSR Certification | ✔ Accessibility |
| Last evaluated | April 12, 2021 (1615 days ago) |
| Attribute Category | Attribute |
|---|---|
| Target | |
| Type of Simulated Data | |
| Variations | |
| Simulation Method | |
| Input | |
| Data Type | |
| File format | |
| Output | |
| Data Type | Methylation, 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 | |
| License | GNU Public License, |
| GSR Certification | Accessibility, Documentation, Application, |
Number of Primary Citations: 1
Number of Non-Primary Citations: 7
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, Jan. 5, 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, Feb. 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, March 1, 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, March 1, 2020 [Abstract]
2019
Hadi Fanaee, Magne Thoresen, Performance evaluation of methods for integrative dimension reduction, Information Sciences, Aug. 2, 2019 [Abstract]
Fanaee-T H, Thoresen M, Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization., Bioinformatics, May 15, 2019 [Abstract]
2017
Chalise P, Fridley BL, Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm., PLoS One, May 1, 2017 [Abstract]