martelotto-lab/STAMP

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging

This repository contains the code used in the STAMP project, focusing on spatial transcriptomics analysis and multiplexing profiling of single cells. The code was utilized to analyze the data presented in the corresponding paper.

Technologies Used

• Spatial Transcriptomics Platforms:
  • NanoString CosMx
  • 10X Genomics Xenium
• Single Cell RNA sequencing Platforms:
  • 10X Genomics Flex

Repository Structure

• misc/
  • BIN.R: Contains functions used throughout the analyses.
  • paths: Contains various paths used in the project.
• stamp_1/, stamp_2/, ..., stamp_n/:
  • Each folder corresponds to a sample and contains the code specific to that sample.
  • Inside each sample folder:
    • Preparation/
      • Scripts for loading the expression matrix and creating SingleCellExperiment objects.
    • QC/
      • Scripts used to perform quality control.
    • Analysis/
      • PreProc.R: Performs preprocessing steps like normalization, feature selection, and dimensionality reduction.
      • Clust.R: Performs clustering analysis.
    • Lvl1/ and Lvl2/:
      • Scripts used for different rounds of cell population annotation.
    • Sub-sample Folders:
      • For samples containing multiple sub-samples (e.g., multiplexed slides), there are folders like Clines/ and PBMC/ (e.g., in stamp_3/), which contain analyses of the respective sub-samples.

R Version

This code was run using R version 4.4.1.

For more details, please refer to the project's paper or contact the authors.