GSR: Editing - interSIM Simulator

You may request changes to this simulator by navigating to the Basic, Details, and Citations/Applications tabs. When you are finished, open the Submit tab. To return back to the simulator view, click interSIM. Finally, please take note of the GSR simulator privacy policy.
interSIM
InterSIM: simulation tool for multiple integrative omic datasets. Comput. Methods Prog. Biomed
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.
Integrative, Clustering, Simulation, Inter, Intra
2.2.0
02-27-2016
07-16-2018
https://cran.r-project.org/web/packages/InterSIM/index.html
None

Attribute Tree Control

Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.

Every sub-attribute is selected
Not all sub-attributes are selected
  • Target
    • Type of Simulated Data
      • Genotype at Genetic Markers
      • Diploid DNA Sequence
      • Haploid DNA Sequence
      • RNA
      • Sex Chromosomes
      • Mitochondrial DNA
      • Protein Sequence
      • Sequencing Reads
      • Phenotype
    • Variations
      • Biallelic Marker
      • Multiallelic Marker
      • Single Nucleotide Variation
      • Amino acid variation
      • Microsatellite
      • Insertion and Deletion
      • CNV
      • Inversion and Rearrangement
      • Alternative Splicing
      • Missing Genotypes
      • Genotype or Sequencing Error
      • Other
  • Simulation Method
    • Standard Coalescent
    • Exact Coalescent
    • Machine Learning
    • Forward-time
    • Resample Existing Data
    • Phylogenetic
    • Gene dropping
    • Other
  • Input
    • Data Type
      • Allele Frequencies
      • Empirical
      • Ancestral Sequence
      • Saved simulation
      • Reference genome
      • Other
    • File format
      • Arlequin
      • CREATE
      • Fstat
      • GDA
      • Genepop
      • MIGRATE
      • MS
      • SAM or BAM
      • NEXUS
      • Phylip
      • STRUCTURE
      • XML
      • Tree Sequence
      • Program Specific
      • Other
  • Output
    • Data Type
      • Genotype or Sequence
      • Phenotypic Trait
      • Individual Relationship
      • Demographic
      • Mutation
      • Methylation
      • Gene Expression
      • Protein Expression
      • Linkage Disequilibrium
      • Diversity Measures
      • Fitness
      • Sequencing Reads
        • Illumina
        • Roche 454
        • SOLiD
        • IonTorrent
        • PacBio
        • Nanopore
        • Other
      • Other
    • File Format
      • Arlequin
      • Fasta or Fastq
      • Fstat
      • Genepop
      • Linkage
      • MIGRATE
      • MS
      • PED
      • Phylip
      • NEXUS
      • STRUCTURE
      • VCF
      • SAM or BAM
      • Tree Sequence
      • Program Specific
      • Other
    • Sample Type
      • Random or Independent
      • Sibpairs, Trios and Nuclear Families
      • Extended or Complete Pedigrees
      • Case-control
      • Longitudinal
      • Other
  • Phenotype
    • Trait Type
      • Binary or Qualitative
      • Quantitative
      • Multiple
    • Determinants
      • Single Genetic Marker
      • Multiple Genetic Markers
      • Sex-linked
      • Gene-Gene Interaction
      • Environmental Factors
      • Gene-Environment Interaction
  • Evolutionary Features
    • Demographic
      • Population Size Changes
        • Constant Size
        • Exponential Growth or Decline
        • Logistic Growth
        • Bottleneck
        • Carrying Capacity
        • User Defined
      • Gene Flow
        • Stepping Stone Models
        • Island Models
        • Continent-Island Models
        • Sex or Age-Specific Migration Rates
        • Influenced by Environmental Factors
        • Admixed Population
        • User-defined Matrix
        • Other
      • Spatiality
        • Discrete Models
        • Continuous Models
        • Landscape Factors
    • Life Cycle
      • Discrete Generation Model
      • Age structured
      • Overlapping Generation
      • User-Defined transition matrices
    • Mating System
      • Random Mating
      • Monogamous
      • Polygamous
      • Haplodiploid
      • Selfing
      • Age- or Stage-Specific
      • Assortative or Disassortative
      • Other
    • Fecundity
      • Constant Number
      • Randomly Distributed
      • Individually Determined
      • Influenced by Environment
      • Other
    • Natural Selection
      • Determinant
        • Single-locus
        • Multi-locus
        • Codon-based
        • Fitness of Offspring
        • Phenotypic Trait
        • Environmental Factors
      • Models
        • Directional Selection
        • Balancing Selection
        • Multi-locus models
        • Epistasis
        • Random Fitness Effects
        • Disruptive
        • Phenotype Threshold
        • Frequency-Dependent
        • Other
    • Recombination
      • Uniform
      • Varying Recombination Rates
      • Gene Conversion Allowed
    • Mutation Models
      • Two-allele Mutation Model
      • Markov DNA Evolution Models
      • k-Allele Model
      • Infinite-allele Model
      • Infinite-sites Model
      • Stepwise Mutation Model
      • Codon and Amino Acid Models
      • Indels and Others
      • Heterogeneity among Sites
      • Others
    • Events Allowed
      • Population Merge and Split
      • Varying Demographic Features
      • Population Events
      • Varying Genetic Features
      • Change of Mating Systems
      • Other
    • Other
      • Phenogenetic
      • Polygenic background
  • Interface
    • Command-line
    • Graphical User Interface
    • Integrated Development Environment
    • Script-based
    • Web-based
  • Development
    • Tested Platforms
      • Windows
      • Mac OS X
      • Linux and Unix
      • Solaris
      • Others
    • Language
      • C or C++
      • Java
      • R
      • Python
      • Perl
      • Visual Basic
      • Other
    • License
      • GNU Public License
      • BSD
      • Creative Commons
      • MIT
      • Other
  • GSR Certification
    • Accessibility
    • Documentation
    • Application
    • Support

Summary of Proposed Changes

Step 2: Review list of proposed attribute addition(s) and subtraction(s).

To Add

    To Remove

      Can't Find the Attribute You Are Looking For?

      If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab.

      You may add citations by pmid, add citations by direct entry, remove citations (using the recycling bin icon), and edit citations (using the rarely seen edit icon) that were originally entered by direct entry.

      Summary of Proposed Changes

      To Add

      To Remove

      Current Citations/Applications

      Hadi Fanaee, Magne Thoresen, Performance evaluation of methods for integrative dimension reduction, Information Sciences, 08-02-2019, https://doi.org/10.1016/j.ins.2019.04.041,, Application
      [Pubmed ID: 27040832], Chalise P, Raghavan R, Fridley BL, InterSIM: Simulation tool for multiple integrative 'omic datasets'., Comput Methods Programs Biomed, 05-01-2016, https://www.ncbi.nlm.nih.gov/pubmed/?term=27040832,Primary Citation
      [Pubmed ID: 28459819], Chalise P, Fridley BL, Integrative clustering of multi-level 'omic data based on non-negative matrix factorization algorithm., PLoS One, 05-01-2017, https://www.ncbi.nlm.nih.gov/pubmed/?term=28459819,, Application
      [Pubmed ID: 30295701], Fanaee-T H, Thoresen M, Multi-insight visualization of multi-omics data via ensemble dimension reduction and tensor factorization., Bioinformatics, 05-15-2019, https://www.ncbi.nlm.nih.gov/pubmed/?term=30295701,, Application
      [Pubmed ID: 31693075], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=31693075,, Application
      [Pubmed ID: 31999549], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=31999549,, Application
      [Pubmed ID: 33402734], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=33402734,, Application
      [Pubmed ID: 33639858], 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, https://www.ncbi.nlm.nih.gov/pubmed/?term=33639858,, Application
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      Please inform the GSR team here if you would like to see an attribute added to the attribute tree (or any other changes to the simulator description system as it exists).