This repo contains tutorials on how to use Seurat, a single-cell analysis toolkit for R.
You'll need to install Docker Desktop. You can find instructions for your operating system here: https://docs.docker.com/get-started/get-docker/
First, change to a folder where you store projects.
cd <location to create project>Then, clone this repository using the following command:
git clone https://github.com/rladies-aurora/scAnalysis_Using_Seurat
cd scAnalysis_Using_SeuratRun the following to build a local Docker image and launch RStudio:
./launch_rstudio.shOnce it's complete, you'll see the following lines in the terminal:
[cont-init.d] done.
[services.d] starting services
[services.d] done.
Visit http://localhost:8787 to access RStudio.
The following notebooks are included in this tutorial:
integration_mapping.Rmd: https://satijalab.org/seurat/articles/integration_mapping.htmlvisualization_vignette.Rmd: https://satijalab.org/seurat/articles/visualization_vignettesingle-cell-easy-tutorial-with-seurat-v5.Rmd: https://biostatsquid.com/single-cell-easy-tutorial-with-seurat-v5/pbmc3k_tutorial.Rmd: https://satijalab.org/seurat/articles/pbmc3k_tutorial