This repository contains software demonstrations of the Bodenmiller laboratory.
Each demo is hosted in its independent branch.
The most current demonstration is compiled as index.html in the docs folder and will automatically be hosted at bodenmillergroup.github.io/demos
The following demos are gathered here:
The workshop given at the EuroBioc2023 conference can be found here. It highlights the use of the cytoviewer and cytomapper R/Bioconductor packages for multiplexed image data visualization in R.
To follow along, please clone the repository
git clone https://github.com/BodenmillerGroup/demos.git
and open the EuroBioc2023_workshop.Rmd file.
The workshop given at the EuroBioc2022 conference can be found here. It highlights the use of the imcRtools R/Bioconductor package for spatial data analysis and visualization.
To follow along, please clone the repository
git clone --single-branch --branch EuroBioc2022 https://github.com/BodenmillerGroup/demos.git
and open the EuroBioc2022_workshop.Rmd file under docs.
The workshop given at the Bioc2022 conference can be found here. It highlights the use of the steinbock python framework and the imcRtools R/Bioconductor package.
To follow along, please clone the repository
git clone --single-branch --branch Bioc2022 https://github.com/BodenmillerGroup/demos.git
and open the Bioc2022_workshop.Rmd file under docs.
The workshop given at the Bioc2021 conference can be found here. It highlights the use of the cytomapper package.
The cytomapper demonstration as presented at the useR! 2021 conference can be found here. The presentation is hosted at https://nilseling.github.io/useR2021_cytomapper
The Indiana O’Brien Center Microscopy Workshop on the cytomapper package was hosted between 7th and 10th June 2021. All resources for the demonstration can be found here. Please follow the analysis script to reproduce the presented demo.