├── .gitignore ├── Dockerfile ├── LICENSE ├── Procfile ├── README.md ├── Screenshot.png ├── app.py ├── computations.py ├── computations_mouse.py ├── doench_score.py ├── emailing.py ├── generate_GRCm38_exons.py ├── helpers ├── __init__.py └── mongo.py ├── index.html ├── install.sh ├── package.json ├── remove_guides_with_off_target.py ├── requirements.txt ├── routes.py ├── run-redis.sh ├── run.sh ├── seperate_exons.py ├── seperate_exons_mus.py ├── seq_generator.py ├── seq_generator_mus.py ├── settings.py ├── static ├── .gitignore ├── css │ ├── .gitignore │ ├── app.less │ ├── beta-ribbon.css │ └── libs │ │ ├── angular-busy.css │ │ └── select.css ├── data │ ├── .gitignore │ ├── functional_tests │ │ ├── expression_on_target_correlation.py │ │ ├── gtex_assists_exon_selection.py │ │ ├── num_exons_targeted.py │ │ ├── on_target_contribution.py │ │ ├── random_guides.py │ │ ├── random_guides_domains.py │ │ ├── speed_benchmarking.py │ │ └── speed_benchmarking_automated.py │ ├── gtex │ │ ├── generate_exons.py │ │ ├── gtex_mouse │ │ │ ├── CCDS_coords.csv │ │ │ ├── ENSMUSG-CCDS.txt │ │ │ ├── exon_info.p │ │ │ ├── generate_exons.py │ │ │ ├── generate_exons_2.py │ │ │ ├── refGene_mouse.txt │ │ │ └── test_multiple.py │ │ ├── refGene.txt │ │ ├── refGene_GRCm38.txt │ │ └── refGene_base.txt │ └── pre_processed │ │ ├── .gitignore │ │ ├── BioMart_Genes_Setup.ipynb │ │ ├── CDS │ │ ├── CCDS_coords.csv │ │ ├── ENSG-CCDS_hum.txt │ │ ├── ccds_coords_hum.txt │ │ └── create_ensg_startstop_hum.py │ │ ├── additional_scripts │ │ ├── CFD_Scoring │ │ │ ├── README_v0.pdf │ │ │ ├── __init__.py │ │ │ ├── cfd-score-calculator-vanilla.py │ │ │ ├── cfd-score-calculator.py │ │ │ ├── check_nums.py │ │ │ ├── g-score-human.py │ │ │ ├── g-score-mouse.py │ │ │ ├── mismatch_score.pkl │ │ │ ├── pam_scores.pkl │ │ │ └── plots.py │ │ ├── GUIDES_figures_CFD │ │ │ ├── .DS_Store │ │ │ ├── .ipynb_checkpoints │ │ │ │ └── Untitled-checkpoint.ipynb │ │ │ ├── Untitled.ipynb │ │ │ ├── all_scores.pdf │ │ │ ├── all_scores_hum.p │ │ │ ├── all_scores_lin.pdf │ │ │ ├── all_scores_log.pdf │ │ │ ├── all_scores_mus.p │ │ │ ├── figures.py │ │ │ ├── figures_mus.py │ │ │ ├── figures_visualize.py │ │ │ ├── selected_scores.pdf │ │ │ ├── selected_scores_hum.p │ │ │ ├── selected_scores_lin.pdf │ │ │ ├── selected_scores_log.pdf │ │ │ ├── selected_scores_mus.p │ │ │ ├── tf_guides_hum.csv │ │ │ ├── tf_guides_mus.csv │ │ │ ├── tf_guides_old.csv │ │ │ └── violin.pdf │ │ └── generation │ │ │ ├── compile_exome.py │ │ │ ├── compile_exome_2.py │ │ │ ├── count_guides_histogram.py │ │ │ ├── count_guides_off_target.py │ │ │ ├── exome_test.py │ │ │ ├── homopolymer_remove.py │ │ │ ├── process.py │ │ │ ├── remove_guides_with_off_target.py │ │ │ └── remove_guides_with_off_target_2.py │ │ ├── doench_score.py │ │ ├── generate_GRCh37_genes.py │ │ ├── generate_GRCm38_genes.py │ │ ├── generate_GRCm38_genes_2.py │ │ ├── genes_list.json │ │ ├── genes_list_GRCm38.txt │ │ ├── genes_list_GRCm38_processed.txt │ │ ├── get_strand_info.py │ │ ├── get_strand_info_GRCm38.py │ │ ├── mart_export_hum.txt │ │ ├── mart_export_hum_2.txt │ │ ├── mart_export_mus.txt │ │ ├── mart_export_mus_2.txt │ │ ├── mismatch_score.pkl │ │ ├── non_targeting_format.py │ │ ├── non_targeting_hum.json │ │ ├── non_targeting_mus.json │ │ ├── non_targeting_unformatted_hum.txt │ │ ├── non_targeting_unformatted_mus.txt │ │ ├── pam_scores.pkl │ │ ├── precompute_df_gene.py │ │ ├── precompute_exon_expression.py │ │ ├── precompute_guides_cpickle.py │ │ ├── precompute_guides_json.py │ │ ├── precompute_guides_msgpack.py │ │ ├── precompute_guides_msgpack_10bp.py │ │ ├── precompute_guides_msgpack_CFD+FD.py │ │ ├── precompute_guides_msgpack_CFD.py │ │ ├── precompute_guides_msgpack_CFD_mus.py │ │ ├── precompute_guides_msgpack_GRCm38.py │ │ ├── precompute_guides_msgpack_all.py │ │ ├── strand_info.p │ │ ├── strand_info_GRCm38.p │ │ └── transform_GRCm38.py ├── font │ ├── AndaleMono.ttf │ ├── LiberationSans-Bold.ttf │ ├── LiberationSans-BoldItalic.ttf │ ├── LiberationSans-Italic.ttf │ ├── franklin-gothic-book-compressed.otf │ ├── franklin-gothic-book-condensed.otf │ ├── franklin-gothic-book-regular.otf │ ├── franklin-gothic-book.otf │ ├── franklin-gothic-lt-book-compressed-regular.otf │ └── liberation-sans-regular.ttf ├── img │ ├── double-helix-spin.gif │ ├── favicon.ico │ ├── zlab-logo-invert.psd │ ├── zlab-logo.png │ └── zlab-logo.psd ├── js │ ├── .gitignore │ ├── app.js.coffee │ ├── controllers │ │ ├── about.js.coffee │ │ ├── designer.js.coffee │ │ └── index.js.coffee │ ├── directives │ │ ├── .keep │ │ ├── drawIndividualExon.js.coffee │ │ ├── expressionBarChart.js.coffee │ │ ├── grow-shrink-arrow.js.coffee │ │ ├── guidesBarChart.js.coffee │ │ └── selectAllCheckbox.js.coffee │ ├── filters │ │ ├── .keep │ │ ├── normalizeExons.js.coffee │ │ ├── numFilter.js.coffee │ │ └── propsFilter.js.coffee │ ├── libs │ │ ├── angular-busy.js │ │ └── select.js │ └── services │ │ ├── .keep │ │ └── 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