SRT-Server: Powering the analysis of spatially resolved transcriptomics studies

Overview

We develop SRT-Server to perform the analysis of spatial resolved transcriptomics (SRT) data. It includes quality control (QC), spatially variable gene detection (SVG), deconvolution (DECON and DECON_PY), cell typing (CT), spatial domain detection (SDD), differential gene expression analysis (DEG), gene set enrichment analysis (GSEA), cell-cell communication identification (CCC) and pseudo-time trajectory inference (TRAJ).
The user can use the server to visit the website: https://spatialtranscriptomicsanalysis.com

Update log

• Version 3.1 (Nov 2023)
  We update the Example Data webpage, and add downloading function.
  
  • For Example Data webpage, we add the demo video for quick start and three case studies and add the Case Study 2.
    
  • For Debug buttom, we add the result downloding.
    
• Version 3.0 (Oct 2023)
  We update the DECON_PY and TRAJ module, add the Tutorial webpage and Example Data webpage, and debug some errors.
  
  • For DECON_PY, we add two methods: cell2location and Tangram.
    
  • For TRAJ, we set DECON as another upstream module, which estimates the pseudo-time trajectory in one cell type.
    
  • For Tutorial webpage, we included three parts to describe each module: i) a brief introduction and description of the module; ii) the analysis component; iii) the plot component.
    
  • For Example Data webpage, we included three parts: i) Quick Start; ii) Case Study 1; iii) Case Study 3. In the two case studies, we added Demo Video to show the analytic procedure and parameter setting.
    
• Version 2.2 (Apr 2023)
  We update the reference panels of single cell RNA-seq data and marker data. Totally, we collect 51 datasets for DECON and CT-Annot. We fix some bugs in DECON and CCC_Plot modules. We deploy the server on Tencent Cloud.
  
• Version 2.1 (Feb 2023)
  We update R into version 4.2.2. We added the “Without login” function for SRT-Server. SRT-Server in “Without login” setting only give user the download link of result, and the analysis flow chart and parameter settings are not saved when the page closed.
  
• Version 2.0 (Jan 2023)
  We update R into version 4.2.1 and fix some bugs. We combine the Annot module to CT module.
  
• Version 1.0 (Dec 2022)
  We first build the SRT-Server to power the spatial resolved transcriptomics (SRT) data analysis.

Q&A

If there are any problems for SRT-Server, please feel free to ask here. We will ask you as soon as possible.

Citation

If you used our server, please cite the our paper:
Sheng Yang, Xiang Zhou. SRT-Server: powering the analysis of spatially resolved transcriptomics studies. Genome Med . 2024 Jan 26;16(1):18