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GSR: Simulator - SRTsim
| Attribute | Value |
|---|---|
| Title | SRTsim |
| Short Description | SRTsim is an independent, reproducible, and flexible Spatially Resolved Transcriptomics (SRT) simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. |
| Long Description | SRTsim is an independent, reproducible, and flexible SRT simulation framework that can be used to facilitate the development of SRT analytical methods for a wide variety of SRT-specific analyses. It utilizes spatial localization information to simulate SRT expression count data in a reproducible and scalable fashion. Two major simulation schemes are implemented in SRTsim: reference-based and reference-free. Available both as an R package and a website: https://jiaqiangzhu.shinyapps.io/srtsim/ |
| Keywords | SRT simulator, spatial localization, reference-based, reference-free, SRT expression count data |
| Version | 0.99.6 |
| Project Started | 2022 |
| Last Release | 2 years, 8 months ago |
| Homepage | https://github.com/xzhoulab/SRTsim |
| Citations | Zhu J, Shang L, Zhou X, SRTsim: spatial pattern preserving simulations for spatially resolved transcriptomics., Genome Biol, March 3, 2023 [ 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, |
| 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, Web-based, |
| Development | |
| Tested Platforms | |
| Language | R, |
| License | GNU Public License, |
| GSR Certification |
Number of Primary Citations: 1
Number of Non-Primary Citations: 0
No example publication using SRTsim has been provided.
Please propose new citations if you are aware of publications that use this software.