├── .gitignore ├── .gitmodules ├── .readthedocs.yaml ├── LICENSE ├── PHLEX_setup.nf ├── README.rst ├── docs ├── Makefile ├── make.bat └── source │ ├── TYPEx.rst │ ├── _files │ ├── ReadTheDocs_Tutorial.pdf │ ├── images │ │ ├── MCCS.png │ │ ├── MCCS_rationale.png │ │ ├── NISD.png │ │ ├── consensus.png │ │ ├── deep-imcyto_jellybean.png │ │ ├── deep-imcyto_overview.png │ │ ├── figure1_zoo_wbg.png │ │ ├── figure1_zoom.png │ │ ├── nuclear_preprocess.png │ │ ├── pseudoHE.png │ │ ├── qc_mode.png │ │ ├── segmentation2.png │ │ ├── simple_seg_marker_plots.png │ │ ├── spatial2.png │ │ ├── spatial_cluster_plot.png │ │ ├── spatial_clustering.png │ │ ├── spatial_phlex_input.png │ │ ├── typing3.png │ │ └── typing4.png │ └── params.csv │ ├── api.rst │ ├── conf.py │ ├── deep-imcyto.rst │ ├── guides.rst │ ├── index.rst │ ├── intro.rst │ ├── overview.rst │ ├── quickstart.rst │ ├── requirements.txt │ ├── spatialPHLEX.rst │ ├── tutorial.rst │ └── usage.rst ├── main.nf ├── nextflow.config └── runPHLEX.sh 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