This repository contains the vignettes and methods developed for the BioSys course.
To access the course final report please click [Portuguese]: Final report
Or download the final report PDF [Portuguese]: Relatorio_FlavioKessler_BioSys.pdf
You can also download the project presentation PDF [Portuguese]: Apresentacao_FlavioKessler_BioSys.pdf
The framework of this project followed three steps:
(i) Process the stxbrain dataset from Seurat and save it as a normalized GraphSpace object, see Setup vignette
(ii) Compute cell-cell communication using CellChat package and store spot-to-spot ligand-receptor pairs, see CellChat vignette
(iii) With stxbrain and all ligand-receptor pairs datasets, the visualization of cell-cell communication in spatial transcriptomics data were performed using PathwaySpace. Please, see PathwaySpace cell communication vignette
The vignette demonstrates the use of R for spatial transcriptomics analysis and visualization, focusing in cell-cell communication.
- CellChat_ProximityNetwork_PathwaySpace.Rmd: main R Markdown file.
- bibliography.bib: references cited in the vignette.
- CellChat_ProximityNetwork_PathwaySpace.html: rendered vignette
- spot-spot_commu_Allbrain.rds: data with all spot-spot cell communications, retrieved from CellChat
- stxbrain_Normalized_GraphSpace.RData: Normalized GraphSpace object of stxbrain
The analysis was written in R and requires the following packages: ggplot2, igraph, CellChat, Seurat, RGraphSpace and PathwaySpace