├── GI_CBL-CNN1_and_other_examples.ipynb ├── GI_DUSP9-MAPK1-ETS2_example.ipynb ├── GI_activation_of_neighboring_genes.ipynb ├── GI_dimensionality_reduction_and_statistics.ipynb ├── GI_downsampling_analysis.ipynb ├── GI_generate_populations.ipynb ├── GI_model_fits.ipynb ├── GI_optimal_umap.ipynb ├── GI_orienting_buffering_interactions.ipynb ├── GI_prediction.ipynb ├── GI_prediction_performance_comparison.ipynb ├── GI_sgRNA_performance.ipynb ├── LICENSE ├── README.md ├── data_sharing ├── 20180821_guides_chosen_for_perturbseq.csv ├── ARCHS4_Tissues_table.txt ├── K562 D6 facs experiment.xlsx ├── cellranger-GRCh38-1.2.0_only_genes.gtf ├── comparisons_to_other_imputation_methods_stats.pkl ├── erythroid_ARCHS4_Tissues_table.txt ├── erythroid_Human_Gene_Atlas_table.txt ├── maps_random_sampling_corrs.csv ├── myeloid_ARCHS4_Tissues_table.txt ├── myeloid_GO_Biological_Process_2018_table.txt ├── myeloid_Human_Gene_Atlas_table.txt ├── optimal_umap_layout.csv └── regr_fits_final.csv ├── figures └── PLACEHOLDER.txt ├── final_emaps ├── 20160125_CRISPRa_doubles_oligos.txt ├── 20180821_guides_chosen_for_perturbseq.csv ├── CRISPRa_epistasis_GBC_final_corrected.xlsx ├── filter0 │ ├── CRISPRa_K562_emap_gene.txt │ ├── CRISPRa_K562_emap_gene_sign_flip.txt │ ├── CRISPRa_K562_emap_sgRNA_nonegs.txt │ ├── CRISPRa_K562_emap_sgRNA_perturbseq.txt │ ├── CRISPRa_K562_emap_sgRNA_wnegs.txt │ ├── CRISPRa_K562_phenotypeMatrix_gene.txt │ ├── CRISPRa_K562_replicate1_allphenotypes.txt │ ├── CRISPRa_K562_replicate1_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicate1_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicate1_singlePhenotypes.txt │ ├── CRISPRa_K562_replicate1_singlePhenotypes_abbaAveraged.txt │ ├── CRISPRa_K562_replicate2_allphenotypes.txt │ ├── CRISPRa_K562_replicate2_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicate2_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicate2_singlePhenotypes.txt │ ├── CRISPRa_K562_replicate2_singlePhenotypes_abbaAveraged.txt │ ├── CRISPRa_K562_replicateAverage_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicateAverage_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicateAverage_singlePhenotypes.txt │ ├── CRISPRa_K562_replicateAverage_singlePhenotypes_abbaAveraged.txt │ └── CRISPRa_K562_sgRNA_to_gene.txt ├── filter15 │ ├── CRISPRa_K562_emap_gene.atr │ ├── CRISPRa_K562_emap_gene.cdt │ ├── CRISPRa_K562_emap_gene.gtr │ ├── CRISPRa_K562_emap_gene.jtv │ ├── CRISPRa_K562_emap_gene.txt │ ├── CRISPRa_K562_emap_gene_sign_flip.atr │ ├── CRISPRa_K562_emap_gene_sign_flip.cdt │ ├── CRISPRa_K562_emap_gene_sign_flip.gtr │ ├── CRISPRa_K562_emap_gene_sign_flip.jtv │ ├── CRISPRa_K562_emap_gene_sign_flip.txt │ ├── CRISPRa_K562_emap_sgRNA_nonegs.atr │ ├── CRISPRa_K562_emap_sgRNA_nonegs.cdt │ ├── CRISPRa_K562_emap_sgRNA_nonegs.gtr │ ├── CRISPRa_K562_emap_sgRNA_nonegs.jtv │ ├── CRISPRa_K562_emap_sgRNA_nonegs.txt │ ├── CRISPRa_K562_emap_sgRNA_perturbseq.txt │ ├── CRISPRa_K562_emap_sgRNA_wnegs.txt │ ├── CRISPRa_K562_phenotypeMatrix_gene.txt │ ├── CRISPRa_K562_replicate1_allphenotypes.txt │ ├── CRISPRa_K562_replicate1_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicate1_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicate1_singlePhenotypes.txt │ ├── CRISPRa_K562_replicate1_singlePhenotypes_abbaAveraged.txt │ ├── CRISPRa_K562_replicate2_allphenotypes.txt │ ├── CRISPRa_K562_replicate2_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicate2_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicate2_singlePhenotypes.txt │ ├── CRISPRa_K562_replicate2_singlePhenotypes_abbaAveraged.txt │ ├── CRISPRa_K562_replicateAverage_phenotypeMatrix.txt │ ├── CRISPRa_K562_replicateAverage_phenotypeMatrix_abbaAveraged.txt │ ├── CRISPRa_K562_replicateAverage_singlePhenotypes.txt │ ├── CRISPRa_K562_replicateAverage_singlePhenotypes_abbaAveraged.txt │ └── CRISPRa_K562_sgRNA_to_gene.txt ├── perturbseq_single_phenotype_table.csv ├── processed_emap.csv ├── processed_fitnesses.csv ├── 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