├── .dockerignore ├── .gitignore ├── 2018_paper_materials ├── README.txt └── scripts │ ├── PBNPA │ └── run_PBNPA_all.py │ ├── bagel │ ├── BAGEL-calc_foldchange.py │ ├── collate_bagel_results.py │ └── run_bagel.py │ ├── ceres │ ├── ceres_avana.R │ ├── ceres_avana_col.R │ ├── ceres_avana_mel.R │ ├── ceres_avana_melcol.R │ ├── ceres_avana_rand.R │ ├── ceres_gecko2.R │ ├── ceres_gecko2_rand.R │ └── make_logfold_gct.py │ ├── create_random_lines.py │ ├── jacks │ ├── combine_single_jacks.py │ ├── leaveoneout_reference_test.py │ ├── run_JACKS_single.py │ ├── sample_jacks_screen.py │ └── sample_jacks_screen_xs.py │ ├── mageck │ ├── collate_mageck_results.py │ └── run_mageck.py │ ├── mageck_mle │ └── run_mageck_mle.py │ ├── meanfc │ └── run_MeanFC.py │ └── screenBEAM │ ├── run_screenBEAM.R │ └── run_screenbeam_all.py ├── LICENSE ├── README.md ├── jacks ├── LICENSE.txt ├── README.md ├── example-small │ ├── example_count_data.tab │ └── example_repmap.tab ├── example │ ├── NEGv1.txt │ ├── example_count_data.tab │ ├── example_grna_JACKS_results.txt │ ├── example_repmap.tab │ ├── example_repmap_matched_ctrls.tab │ └── example_repmap_oneonly.tab ├── jacks │ ├── __init__.py │ ├── infer.py │ ├── jacks_io.py │ ├── plot_infer.py │ └── preprocess.py ├── plot_heatmap.py ├── run_JACKS.py └── setup.py ├── reference_grna_efficacies ├── avana_grna_JACKS_results.txt ├── gecko2_grna_JACKS_results.txt ├── tko_grna_JACKS_results.txt ├── whitehead_grna_JACKS_results.txt └── yusa_v10_grna_JACKS_results.txt └── server ├── Dockerfile ├── __init__.py ├── app.py ├── k8s ├── deployment.yaml ├── pv.yaml ├── pvc.yaml └── service.yaml ├── requirements.txt ├── static ├── app.css ├── app.js └── sanger_logo.jpg ├── templates ├── base.html ├── index.html ├── plot.html └── results.html └── uwsgi.ini /.dockerignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/.dockerignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .idea 2 | *.egg-info 3 | __pycache__ -------------------------------------------------------------------------------- /2018_paper_materials/README.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/README.txt -------------------------------------------------------------------------------- /2018_paper_materials/scripts/PBNPA/run_PBNPA_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/PBNPA/run_PBNPA_all.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/bagel/BAGEL-calc_foldchange.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/bagel/BAGEL-calc_foldchange.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/bagel/collate_bagel_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/bagel/collate_bagel_results.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/bagel/run_bagel.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/bagel/run_bagel.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_avana.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_avana.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_avana_col.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_avana_col.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_avana_mel.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_avana_mel.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_avana_melcol.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_avana_melcol.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_avana_rand.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_avana_rand.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_gecko2.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_gecko2.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/ceres_gecko2_rand.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/ceres_gecko2_rand.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/ceres/make_logfold_gct.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/ceres/make_logfold_gct.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/create_random_lines.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/create_random_lines.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/jacks/combine_single_jacks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/jacks/combine_single_jacks.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/jacks/leaveoneout_reference_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/jacks/leaveoneout_reference_test.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/jacks/run_JACKS_single.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/jacks/run_JACKS_single.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/jacks/sample_jacks_screen.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/jacks/sample_jacks_screen.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/jacks/sample_jacks_screen_xs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/jacks/sample_jacks_screen_xs.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/mageck/collate_mageck_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/mageck/collate_mageck_results.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/mageck/run_mageck.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/mageck/run_mageck.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/mageck_mle/run_mageck_mle.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/mageck_mle/run_mageck_mle.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/meanfc/run_MeanFC.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/meanfc/run_MeanFC.py -------------------------------------------------------------------------------- /2018_paper_materials/scripts/screenBEAM/run_screenBEAM.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/screenBEAM/run_screenBEAM.R -------------------------------------------------------------------------------- /2018_paper_materials/scripts/screenBEAM/run_screenbeam_all.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/2018_paper_materials/scripts/screenBEAM/run_screenbeam_all.py -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/README.md -------------------------------------------------------------------------------- /jacks/LICENSE.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/LICENSE.txt -------------------------------------------------------------------------------- /jacks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/README.md -------------------------------------------------------------------------------- /jacks/example-small/example_count_data.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example-small/example_count_data.tab -------------------------------------------------------------------------------- /jacks/example-small/example_repmap.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example-small/example_repmap.tab -------------------------------------------------------------------------------- /jacks/example/NEGv1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/NEGv1.txt -------------------------------------------------------------------------------- /jacks/example/example_count_data.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/example_count_data.tab -------------------------------------------------------------------------------- /jacks/example/example_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/example_grna_JACKS_results.txt -------------------------------------------------------------------------------- /jacks/example/example_repmap.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/example_repmap.tab -------------------------------------------------------------------------------- /jacks/example/example_repmap_matched_ctrls.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/example_repmap_matched_ctrls.tab -------------------------------------------------------------------------------- /jacks/example/example_repmap_oneonly.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/example/example_repmap_oneonly.tab -------------------------------------------------------------------------------- /jacks/jacks/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /jacks/jacks/infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/jacks/infer.py -------------------------------------------------------------------------------- /jacks/jacks/jacks_io.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/jacks/jacks_io.py -------------------------------------------------------------------------------- /jacks/jacks/plot_infer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/jacks/plot_infer.py -------------------------------------------------------------------------------- /jacks/jacks/preprocess.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/jacks/preprocess.py -------------------------------------------------------------------------------- /jacks/plot_heatmap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/plot_heatmap.py -------------------------------------------------------------------------------- /jacks/run_JACKS.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/run_JACKS.py -------------------------------------------------------------------------------- /jacks/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/jacks/setup.py -------------------------------------------------------------------------------- /reference_grna_efficacies/avana_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/reference_grna_efficacies/avana_grna_JACKS_results.txt -------------------------------------------------------------------------------- /reference_grna_efficacies/gecko2_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/reference_grna_efficacies/gecko2_grna_JACKS_results.txt -------------------------------------------------------------------------------- /reference_grna_efficacies/tko_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/reference_grna_efficacies/tko_grna_JACKS_results.txt -------------------------------------------------------------------------------- /reference_grna_efficacies/whitehead_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/reference_grna_efficacies/whitehead_grna_JACKS_results.txt -------------------------------------------------------------------------------- /reference_grna_efficacies/yusa_v10_grna_JACKS_results.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/reference_grna_efficacies/yusa_v10_grna_JACKS_results.txt -------------------------------------------------------------------------------- /server/Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/Dockerfile -------------------------------------------------------------------------------- /server/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /server/app.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/app.py -------------------------------------------------------------------------------- /server/k8s/deployment.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/k8s/deployment.yaml -------------------------------------------------------------------------------- /server/k8s/pv.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/k8s/pv.yaml -------------------------------------------------------------------------------- /server/k8s/pvc.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/k8s/pvc.yaml -------------------------------------------------------------------------------- /server/k8s/service.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/k8s/service.yaml -------------------------------------------------------------------------------- /server/requirements.txt: -------------------------------------------------------------------------------- 1 | flask 2 | jinja2 3 | wtforms 4 | celery 5 | redis 6 | -------------------------------------------------------------------------------- /server/static/app.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/static/app.css -------------------------------------------------------------------------------- /server/static/app.js: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/static/app.js -------------------------------------------------------------------------------- /server/static/sanger_logo.jpg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/static/sanger_logo.jpg -------------------------------------------------------------------------------- /server/templates/base.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/templates/base.html -------------------------------------------------------------------------------- /server/templates/index.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/templates/index.html -------------------------------------------------------------------------------- /server/templates/plot.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/templates/plot.html -------------------------------------------------------------------------------- /server/templates/results.html: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/templates/results.html -------------------------------------------------------------------------------- /server/uwsgi.ini: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/felicityallen/JACKS/HEAD/server/uwsgi.ini --------------------------------------------------------------------------------