sgosline/scrna-seq-qc repository overview

⁠scRNAseqQC

Class and function definitions are contained in the QC.py file

Tutorial contained in .ipynb

⁠Under development

Currently we are still updating the interactive mode of this to enable it to run unsupervised.

⁠Requirements

To run this you will need to install:

• Docker: this is required to run the container
• Workflow engine: the code written in cwl will require something like cwl-runner or toil

You will also need a sample-by-gene comma-delimited matrix. Genes are expected to be in the columsn and samples by row.

⁠To run interactively

python3 run-qc.py -f test_file.csv -q 30 -o test_output

⁠To run via CWL

[add instructions here]

⁠This scRNA-seq quality control pipeline requires python 3, numpy, pandas, scipy, and scanpy installed.