Simsite is a web-based vignettes for illustrating the usage of our simulation pipeline for single-cell and spatial transcriptome data.
The online shiny tool for method selection and data simulation can be accessed here.
Simsite contains three main sections:
Programming usage. All demonstrations and programming environment are in R. It shows the pipeline from environment configuration, parameter estimation, data simulation and output assessment.
References. simmethods is the core package in our project. We collected 49 methods and bundled them into a single package. For each method, we prepared a detailed vignette for users.
Online tool for method selection and simulation. We also provided an interactive website for users to select a suitable simulation method and simulate datasets conveniently.
Install R packages or download Docker images ⬅
Online tool for method selection and data simulation tool ⬅
A Docker image is provided to help users configure the environment easily.
An interactive online tool can be used.
Detailed vignettes for each simulation method using simmethods package.
If you need help or have any issue about our tools and vignettes. Send an email to duohongrui(duohongrui@cqnu.edu.cn) or raise an issue on github.
We are glad to add new simulation methods (especially for simulating spatial transcriptome data) if some methods are innovative and new. If you have the requirements, please tell Hongrui Duo by email(duohongrui@cqnu.edu.cn) or raise an issue for that.