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GSR: Simulator - scDesign3
| Attribute | Value |
|---|---|
| Title | scDesign3 |
| Short Description | scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics |
| Long Description | The R package scDesign3 is an all-in-one single-cell data simulation tool by using reference datasets with different cell states (cell types, trajectories or and spatial coordinates), different modalities (gene expression, chromatin accessibility, protein abundance, DNA methylation, etc), and complex experimental designs. The transparent parameters enable users to alter models as needed; the model evaluation metrics (AIC, BIC) and convenient visualization function help users select models |
| Keywords | spatially resolved transcriptomics, spatial omics, single-cell |
| Version | 1.1.3 |
| Project Started | 2018 |
| Last Release | 1 year, 1 month ago |
| Homepage | https://github.com/SONGDONGYUAN1994/scDesign3 |
| Citations | Song D, Wang Q, Yan G, Liu T, Sun T, Li JJ, scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics., Nat Biotechnol, Feb. 1, 2024 [ Abstract, cited in PMC ] |
| GSR Certification | This simulator has not yet been evaluated for GSR Certification. Learn more about or request GSR Certification. |
| 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 | RNA, Single-Cell Sequencing, |
| Variations | |
| Simulation Method | Resample Existing Data, |
| Input | |
| Data Type | Reference genome, |
| File format | Other, |
| Output | |
| Data Type | |
| Sequencing Reads | Other, |
| File Format | Other, |
| Sample Type | Other, |
| 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 | Script-based, |
| Development | |
| Tested Platforms | Linux and Unix, |
| Language | R, |
| License | MIT, |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using scDesign3 has been provided.
Please propose new citations if you are aware of publications that use this software.