pipeline_dehash.py

Overview

This pipeline dehashes cells which have multiplexed using hash tag oligos (HTOs).

Usage

See Installation and Usage for general information on how to use cgat pipelines.

Configuration

The pipeline requires a configured pipeline.yml file.

Default configuration files can be generated by executing:

cellhub celldb config

Code

cellhub.pipeline_dehash.gmmDemux(infile, outfile)

Run gmmDemux

cellhub.pipeline_dehash.gmmAPI(infiles, outfile)

Register the GMM-Demux results on the API

cellhub.pipeline_dehash.hashCountCSV(infile, outfile)

Make the hash count csv table for demuxEM

cellhub.pipeline_dehash.demuxEM(infile, outfile)

Run demuxEM

cellhub.pipeline_dehash.parseDemuxEM(infile, outfile)

Parse the ridiculous output format from demuxEM.

cellhub.pipeline_dehash.demuxemAPI(infiles, outfile)

Register the demuxEM results on the API