xzhoulab / srtsim

SRTsim

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.

How to install SRTsim

1. Install devtools if necessary

install.packages('devtools')

2. Install SRTsim

devtools::install_github('xzhoulab/SRTsim')

3. Load package

library(SRTsim)

How to cite SRTsim

Jiaqiang Zhu, Lulu Shang and Xiang Zhou#. SRTsim: A simulator for spatially resolved transcriptomics, 2022.

How to use SRTsim

Details in here

srtsim's Issues

Script for generating SE simulation data

Thank you for your amazing work!

In the manuscript, you performed an SE analysis with simulations of layer-specific expressions that are generated in a reference-free fashion. However, I could not seem to understand how to generate similar simulations, as the tutorial only shows how to generate the two datasets in a reference-based manner. If it is not too much trouble, could you please provide the script for generating the layer-specific expressions for the SE analysis?

How to download cell location file?

Hello, thank your work , it helped me a lot.
But I have a question about how to get the cell location file?
It seem to be that the cells location information is not in the shinySRT1 object.

Bug: Lasso selection in grid

In the reference-free shiny app, lasso selections in a grid will always be converted to rectangles.

Thanks!

Reference-free simulation of 10x Visium data

Hi, which parameter setting do you suggest to simulate 10X Visium data in a reference-free grid?
Much appreciated!
Simon

Generate sythetic data with custom locations

First of all, I'd like to express my appreciation for the useful software provided by your project. I've been exploring SRTsim and found it valuable for my work.

I was wondering if it's possible to generate synthetic data by passing custom locations. In my research, I need to use specific user-defined locations for data generation. I noticed that SRTsim currently supports two location layouts, "grid" and "random," in strtsim_newlocs. However, I would like to know if there's a way to pass custom user-defined locations and generate synthetic data based on those locations.

Your insights on this matter would be greatly appreciated.

dashboardthemes package dependency

Please be aware that the dashboardthemes package will no longer be supported and will be taken off CRAN at some point (probably by end-year).

I suggest you migrate to either the "bslib" or "fresh" theming packages, both of which are on CRAN.

shiny error

Hi,

I encountered one error at shinySRT1<-SRTsim_shiny():

An error has occurred!
could not find function "register_theme_dependency"

Could you please provide any insight on this issue? I would greatly appreciate any help you can provide. Thanks!

I cannot open "http://127.0.0.1:4218", any suggestions?