This material is linked to a face-to-face training. It is not intended to be used as e-learning only since it does not contain all the info.
- scater (install via BiocManager::install(‘scater’))
On the first day we use the data set from Antunes et al., 2021. The data can be downloaded from the brain immune atlas. We use the fourth mouse sample (KO and WT) labeled as Mouse GBM citeSeq. Download the Gene-cell count matrix.
On the second day you bring your own data in the form of a count matrix or a Seurat object (or both).
We cannot process bcl files. Contact us if you have issues obtaining a count matrix.
- Slides of the introduction, given by Niels
- Slides of the introduction, given by Irina
- Slides for the basic R script
Scripts and R objects
- Tutorial for the basic script
- R markdown file for the basic script
- Simple basic R script
- Small raw data set as a matrix
- Clean data set as a matrix
- Single Cell Experiment after outlier analysis
- Seurat object before Seurat analysis
- Seurat object after Seurat analysis