├── .gitignore ├── README.md ├── conda.sh ├── example_notebooks ├── example_image_analysis.ipynb ├── example_ngs_analysis.ipynb └── example_pool_design.ipynb ├── example_pool ├── NCBI_ids.tsv ├── X.txt ├── Y.txt ├── Z.txt ├── design.xls ├── kosuri_dialout_primers.csv └── nontargeting.txt ├── install.sh ├── license.txt ├── ops ├── __init__.py ├── annotate.py ├── cellpose.py ├── constants.py ├── external │ ├── __init__.py │ ├── tifffile_new.py │ └── tifffile_old.py ├── features.py ├── filenames.py ├── firesnake.py ├── imports.py ├── imports_ipython.py ├── in_situ.py ├── intake │ ├── __init__.py │ ├── common.py │ └── custom.py ├── io.py ├── ngs.py ├── paper │ ├── cell_idr.py │ ├── fig3.py │ ├── fig4.py │ └── shared.py ├── plates.py ├── pool_design.py ├── process.py ├── qc.py ├── rolling_ball.py ├── screen_stats.py ├── timelapse.py ├── triangle_hash.py ├── utils.py └── visitor1.ttf ├── package-list.txt ├── requirements.txt ├── requirements_gcolab.txt ├── resources ├── CROPseq_NFkB_library.csv ├── Cell_IDR.smk ├── Cell_IDR_files.csv.gz ├── OpticalPooledScreens.smk ├── asperaweb_id_dsa.openssh ├── cellpose_test.yaml ├── example_config_paramsearch_read-calling.yaml ├── example_config_paramsearch_segmentation.yaml ├── example_config_process.yaml ├── experimentC_example.yaml ├── experimentC_fig3_fig4.yaml ├── experimentC_fig3_small.yaml ├── experimentC_fig4_all.yaml ├── experimentC_fig4_small.yaml └── input_files.xlsx ├── scripts ├── fastq2hist.sh ├── format_input.py ├── grep_sg.sh ├── hist.sh ├── paper │ └── FT_D458.smk └── setup_experiment_directory.sh └── setup.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/feldman4/OpticalPooledScreens/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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