This repository contains scripts and vignettes for the SIB days workshop "PASTA: Pattern Analysis for Spatial Omics Data".
In this workshop we will highlight the usefulness and transferability of existing spatial statistics approaches in the context of spatial tissue profiling. Primarily we will discuss point pattern and lattice data analysis using two spatial transcriptomics datasets.
Planned timeline:
| 09:30 - 10:00 | Introduction to spatial omics technologies and PASTA |
| 10:00 - 10:45 | Primer into point pattern analysis |
| 10:45 - 11:15 | Coffee break |
| 11:15 - 12:00 | Primer into lattice data analysis |
| 12:00 - 12:30 | Comparison of approaches; discussion |
In the point pattern and lattice analysis part, you will go through the respective quarto documents (.qmd) that you find in this repo. You will need to have a number of packages installed to run the quarto documents. Please read the instructions for installation below.
Please bring your personal laptop with an installation of R. The R version must be 4.2 or higher and Bioconductor 3.17 or newer. Electrical outlets will be available in the room.
To install all necessary packages please run the following commands in R.
pkgs <- c('SpatialExperiment', 'spatstat.geom', 'spatstat.explore',
'dplyr', 'ggplot2', 'patchwork', 'reshape2', 'Voyager',
'SpatialFeatureExperiment', 'SFEData', 'spdep', 'sf', 'stringr', 'tidyr',
'magrittr','scater')
if (!requireNamespace("BiocManager")) install.packages("BiocManager")
BiocManager::install(pkgs)
In case there are problems installing the software, another option is to use an already-prepared Docker container. This would require you to install Docker on your computer; see here. For Apple M1/M2 users: You need to enable the rosetta2 virtualization feature in docker desktop. To use the docker container, you can download the prepared image and run it as follows:
docker pull markrobinsonuzh/sibdays-pasta:14062024
docker run -e PASSWORD=abc -p 8787:8787 markrobinsonuzh/sibdays-pasta:14062024
Once that is running, go to a web browser and use localhost:8787 to bring up an RStudio instance that is running within the Docker container (username is rstudio, password is as set in the command above). All the software needed for the PASTA workshop is already installed there.
- Martin Emons, PhD Student, Statistical Bioinformatics Group, University of Zurich
- Samuel Gunz, PhD Student, Statistical Bioinformatics Group, University of Zurich
- Mark D. Robinson, Professor of Statistical Genomics, University of Zurich
- Helena L. Crowell, Postdoc, CNAG