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.

conda install seaborn scikit-learn statsmodels numba pytables

conda install -c conda-forge python-igraph louvain