From Kallisto | Bustools workflow counttable to preprocessed Seurat object.
Install Miniconda.
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
kb_seurat_pp.rmd
-> Fill parameters -> Knitrmarkdown::render('kb_seurat_pp.rmd,....
) from R console. The indexing and alignment for RNA Velocity can easily be performed with the scRNA-seq workflow of seq2science.