Here is a collection of the codes i used and/or wrote for my master thesis project. It include scRNA sequencing analysis and multiplex Image analysis.
To get a quick idea of what my master thesis project was, here is a quick summary: "We developed a 9-plex immunofluorescence panel using the Opal™ system and quantitative analysis to evaluate the expression of PD-L1, CD8A, FoxP3, CD163, KRT7, PDGFRB, and CD79A in whole ovarian cancer tissues. An additional slot was left to test new markers with little to no literature describing them in HGSOC. Therefore, in this project, we tested 2 test markers within this multiplex panel to learn more about their expression pattern in the immune environment in the context of HGSOC."
If you are my master thesis reviewer, thanks for coming to check my scripts. Here are some info to make it easier to find the information:
- You will find my full scripts for my scRNAseq re-analysis in: scRNA_seq_analysis.Rmd or click here to see the html version.
- You will find the Qupath and Stardist script in: QuPath scripts
- You will find the downstream image/statistical analysis here: Image_analysis.Rmd
If you, a lucky visitor, has any question on my code or wish to discuss anything and how it could help you don't hesistate to contact me. Lastly, I am quite the beginner and this was my first project ever. I appreciate any feedback and anything you have to teach me.
The Seurat vignette on which my scNRA seq analysis workflow is based can be found here
The Stardist extension used for cell segmentation can be found here