Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools

Install Dependencies

The environment for Step 1 of this protocol require Singularity. The details of this installation can be found in the Step 1 notebook.

The environment for Steps 2 and 3 of this protocol can be installed through the included .yml with the following, which will also initialize a jupyter kernel:

conda env create -f qc_pipe_env.yml
python -m ipykernel install --user --name=qc_pipe

Otherwise, the requirements.txt file can be manually installed In a working Python virtual environment using pip:

pip install -r requirements.txt

Instructions

Step 1

Step 2v1

Step 2v2

Step 3