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Getting started
tschaefers edited this page Jul 8, 2021
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Install Miniconda.
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Install Mamba
conda install mamba -n base -c conda-forge
- Download the newest release of scRNA-seq or clone the repository.
git clone https://github.com/Rebecza/scRNA-seq.git
- Create & activate environment.
cd scRNA-seq/envs
mamba env create -f kb_scrna_R_seurat3.yaml
conda activate kb_scrna_R_seurat3
- Install RStudio (optional)
mamba install -n kb_scrna_R_seurat3 r::rstudio
Note: RStudio should be started from within the conda environment.
- Running
- RStudio: Open
kb_seurat_pp.rmd-> Fill parameters -> Knit
- Command-line: Run
rmarkdown::render('kb_seurat_pp.rmd,....) from R console.