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 | 5 years, 9 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, 05-01-2016 [ Abstract, cited in PMC ] |
GSR Certification | ✔ Accessibility |
Last evaluated | 04-12-2021 (1097 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, 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]