├── .gitignore ├── LICENSE ├── README.md ├── analysis ├── README.md ├── gene_scoring │ ├── README.md │ ├── calc_gene_bfs.py │ ├── compare_models.R │ ├── compare_two_models.R │ ├── determine_effective_case_n.py │ ├── distill_optimization_data.py │ ├── ensemble_classifier.R │ ├── estimate_prior_effect_sizes.R │ ├── eval_or_vs_cnv_counts.R │ ├── gene_scoring_analysis.sh │ ├── gene_scoring_analysis.wdl │ ├── get_underpowered_genes.R │ ├── merge_del_dup_scores.R │ ├── optimize_genes_per_cnv.R │ ├── plot_gene_score_qc.R │ ├── plot_score_feature_cors.R │ ├── score_genes.py │ ├── scores_vs_gnomad-SV.R │ ├── select_hpos.R │ ├── split_genes_by_effect_size.R │ └── variance_vs_counts.R ├── generic_scripts │ ├── fisher_test_single_cohort.R │ └── meta_analysis.R ├── genes │ ├── README.md │ ├── cluster_gene_blocks.py │ ├── compare_gene_burden_models.sh │ ├── constraint_vs_pip.R │ ├── count_cnvs_per_gene.py │ ├── finemap_genes.py │ ├── gene_burden_analysis.sh │ ├── gene_burden_analysis.wdl │ ├── get_significant_genes.R │ ├── get_significant_genes_v2.py │ ├── optimize_cds_overlap.sh │ ├── plot_finemap_coefficients.R │ ├── plot_finemap_results.R │ ├── plot_gene_burden_meta_analysis_p_value_distributions.R │ └── scattered_gene_burden_perm_test.wdl ├── other │ ├── count_cnvs_by_cds.R │ ├── estimate_p_for_fdr.R │ ├── optimize_min_cds.R │ ├── split_phenos_by_severity.R │ └── split_phenos_by_severity.sh ├── paper │ ├── README.md │ ├── plot │ │ ├── gene_association │ │ │ ├── plot_cds_optimization.R │ │ │ ├── plot_finemapped_enrichments.R │ │ │ ├── plot_finemapped_gene_table.R │ │ │ ├── plot_finemapping_distribs.R │ │ │ └── plot_gene_feature_cor_matrix.R │ │ ├── gene_scores │ │ │ ├── driver_gene_prediction.R │ │ │ ├── ds_feature_regressions.R │ │ │ ├── empirical_score_cutoffs.R │ │ │ ├── plot_asd_denovo_cnv_analysis.R │ │ │ ├── plot_dnm_enrichments.R │ │ │ ├── plot_ds_feature_distribs.R │ │ │ ├── plot_ds_model_training_distribs.R │ │ │ ├── plot_gene_set_enrichments.R │ │ │ ├── plot_gnomad-sv_comparisons.R │ │ │ ├── plot_ml_performance.R │ │ │ ├── plot_phaplo_vs_ptriplo_trainingsets.R │ │ │ ├── plot_scores_scatter.R │ │ │ └── score_vs_score_correlations.R │ │ ├── large_segments │ │ │ ├── plot_association_grid.R │ │ │ ├── plot_basic_segment_distribs.R │ │ │ ├── plot_cross_cohort_effect_size_comparisons.R │ │ │ ├── plot_dnm_comparisons.R │ │ │ ├── plot_effect_sizes.R │ │ │ ├── plot_example_miami.R │ │ │ ├── plot_orig_vs_refined_assoc_sizes.R │ │ │ ├── plot_permuted_fdr.R │ │ │ ├── plot_pleiotropy.R │ │ │ ├── plot_seg_attributes_vs_ngenes.R │ │ │ ├── plot_segment_bygene_perms.R │ │ │ ├── plot_segment_permutations.R │ │ │ └── plot_sliding_window_pval_distribs.R │ │ ├── locus_highlights │ │ │ ├── plot_10p14_locus.R │ │ │ ├── plot_CADM2_locus.R │ │ │ └── plot_locus_highlight.R │ │ └── misc │ │ │ ├── plot_cnv_filtering_summary.R │ │ │ ├── plot_dummy_miami.R │ │ │ ├── plot_global_summary.R │ │ │ ├── plot_gnomad_freq_comparisons.R │ │ │ ├── plot_hpo_summary.R │ │ │ ├── plot_mini_feature_matrix.R │ │ │ ├── plot_mini_gene_score_scatter.R │ │ │ └── plot_upset.R │ ├── scripts │ │ ├── gene_association │ │ │ └── shuffle_gene_blocks.py │ │ ├── large_segments │ │ │ ├── annotate_shuffled_seg_gene_blocks.py │ │ │ ├── asc_replication_analysis.R │ │ │ ├── calc_all_seg_stats.py │ │ │ ├── calc_permuted_fdr.single_pheno.R │ │ │ ├── cluster_segments_before_plotting.py │ │ │ ├── compile_segment_table.py │ │ │ ├── get_best_p_per_window.R │ │ │ ├── get_replication_counts.py │ │ │ ├── get_sig_windows.R │ │ │ ├── polish_nahr_labels.R │ │ │ ├── reformat_shuffled_sig_segs.R │ │ │ └── shuffle_segs.py │ │ ├── locus_highlights │ │ │ └── enumerate_locus_highlight_plot_calls.py │ │ └── misc_setup │ │ │ ├── hpo_jaccard.py │ │ │ └── reorder_hpo_terms.py │ ├── shell │ │ ├── ancillary_dataset_curation.sh │ │ ├── cnv_hpo_curation.sh │ │ ├── gene_association_analyses.sh │ │ ├── gene_score_analyses.sh │ │ ├── global_analyses.sh │ │ ├── graphical_abstract_plots.sh │ │ ├── large_segment_analyses.sh │ │ ├── locus_highlight_plots.sh │ │ ├── misc_analyses.sh │ │ ├── prep_release_files.sh │ │ └── prioritze_locus_highlights.sh │ └── wdl │ │ └── large_segments │ │ ├── collect_permuted_fdrs.sliding_windows.wdl │ │ ├── collect_permuted_meta_p_matrices.sliding_windows.wdl │ │ ├── plot_large_seg_perm_analyses.wdl │ │ ├── segment_permutation.wdl │ │ └── segment_permutation_bygene.wdl └── sliding_windows │ ├── README.md │ ├── calc_empirical_fdr.R │ ├── count_cnvs_per_window.py │ ├── get_genes_per_region.py │ ├── get_significant_windows.R │ ├── plot_sliding_window_meta_analysis_p_value_distributions.R │ ├── refine_significant_regions.py │ ├── regions_summary.plot.R │ ├── scattered_sliding_window_perm_test.wdl │ ├── sliding_window_analysis.sh │ └── sliding_window_analysis.wdl ├── config ├── conda_env_config.r_packages.yml └── conda_env_config.yml ├── data_curation ├── CNV │ ├── README.md │ ├── build_cnv_stats_table.py │ ├── collect_cohort_stats.sh │ ├── defragment_cnvs.py │ ├── extract_noncoding_cnvs.py │ ├── extract_noncoding_subsets.sh │ ├── filter_CNV_data.sh │ ├── filter_CNV_data.wdl │ ├── filter_CNVs_singleCohort.wdl │ ├── filter_cnv_bed.py │ ├── find_cand_artifact_sites.R │ ├── flatten_callset.py │ ├── flatten_callsets.sh │ ├── format_CNVs_for_UCSC.sh │ └── plot_cnv_stats_per_cohort.R ├── README.md ├── binned_genome │ ├── README.md │ └── create_genome_bins.sh ├── gene │ ├── README.md │ ├── apply_pext_filter.py │ ├── filter_UTRs.py │ ├── format_genes.sh │ ├── get_canonical_transcripts.py │ ├── get_gene_features.py │ ├── get_gene_metadata.wdl │ ├── get_gnomad-sv_genelists.R │ ├── get_gnomad_genelists.R │ ├── get_noncoding_rnas.py │ ├── get_variable_expressors.py │ ├── join_gene_metadata.R │ ├── parse_clingen_genes.R │ ├── parse_cosmic_genes.R │ ├── parse_ddg2p_genes.R │ ├── preprocess_GTEx.py │ ├── preprocess_REP.py │ ├── print_chromhmm_readme_rows.py │ ├── process_pext.py │ └── process_pext.wdl ├── other │ ├── README.md │ ├── clean_gnomad_mutation_rates.R │ ├── cluster_gds.py │ ├── collapse_segdup_pairs.py │ ├── curate_asc_dnms.py │ ├── curate_asc_spark_denovo_cnvs.py │ ├── curate_asc_spark_rare_cnvs.py │ ├── curate_control_probesets.sh │ ├── curate_ddd_dnms.py │ ├── curate_gnomad_sv_gene_counts.py │ ├── curate_hgdp_svs.sh │ ├── curate_known_gds.sh │ ├── curate_redin_bcas.py │ ├── get_common_control_cnv_regions.py │ ├── match_segs_by_gene_content.py │ ├── parse_clingen_regions.R │ ├── predict_nahr_cnvs.sh │ ├── preprocess_uniprot_data.py │ ├── probe_based_exclusion.py │ ├── reformat_hgdp_vcf.py │ ├── rewrite_vcf_coords.py │ └── vcf2bed_merge.py └── phenotype │ ├── HPO_obo_to_tsv.py │ ├── README.md │ ├── collapse_HPO_tree.py │ ├── convert_phenotypes_to_hpo.sh │ ├── count_samples_by_pheno_list.py │ ├── filter_HPO_per_sample.py │ ├── filter_coocurrence_table.py │ ├── gather_hpo_per_cohort_table.py │ ├── icd10_to_indication.py │ ├── indication_to_HPO.py │ ├── plot_hpo_per_cohort.R │ └── tabulate_ukbb_icd10_dictionary.py ├── docker ├── Dockerfile ├── README.md ├── rcnv-base │ └── Dockerfile └── rcnv │ └── Dockerfile ├── refs ├── CHOP.blacklist.DEL.bed ├── CHOP.blacklist.DUP.bed ├── Decipher_GD.bed.gz ├── Dittwald_2013_GD.bed.gz ├── Girirajan_2012_GD.bed.gz ├── Kaminsky_2011_GD.bed.gz ├── Li_2020_GD.bed.gz ├── Stefansson_2014_GD.bed.gz ├── UKBB_GD.Owen_2018.DEL.bed.gz ├── UKBB_GD.Owen_2018.DUP.bed.gz ├── UKBB_GD.Owen_2018.bed.gz ├── hpo │ ├── break_hpo_mappings.tsv │ ├── eligible_hpo_terms.txt │ ├── manual_hpo_pair_similarity_drops.tsv │ └── supplementary_hpo_mappings.tsv ├── icd10 │ ├── UKBB_ICD_sample_blacklist.txt │ ├── UKBB_ICD_term_blacklist.txt │ └── UKBB_ICD_term_whitelist.txt ├── lit_GDs.all.DEL.bed.gz ├── lit_GDs.all.DUP.bed.gz └── rCNV_sample_counts.txt ├── source ├── README.md ├── rCNV2 │ ├── .Rbuildignore │ ├── DESCRIPTION │ ├── NAMESPACE │ ├── R │ │ ├── assoc.R │ │ ├── constants.R │ │ ├── data_io.R │ │ ├── gene_assoc_plot.R │ │ ├── gene_assoc_utils.R │ │ ├── gene_score_plot.R │ │ ├── gene_score_utils.R │ │ ├── highlight_plot.R │ │ ├── highlight_utils.R │ │ ├── large_seg_plot.R │ │ ├── large_seg_utils.R │ │ ├── manhattan_qq.R │ │ ├── other_utils.R │ │ ├── overview_plot_utils.R │ │ ├── plot_utils.R │ │ └── zzz.R │ ├── man │ │ ├── add.xaxis.to.perm.plot.Rd │ │ ├── build.fisher.lookup.table.Rd │ │ ├── calc.or.Rd │ │ ├── calc.perm.p.Rd │ │ ├── calc.segs.dat.Rd │ │ ├── categorize.genes.Rd │ │ ├── classify.genes.by.score.Rd │ │ ├── color.points.by.density.Rd │ │ ├── combine.dnms.Rd │ │ ├── combine.single.cohort.assoc.stats.Rd │ │ ├── credsets.scatter.Rd │ │ ├── dens.scatter.Rd │ │ ├── estimate.cohort.inflation.Rd │ │ ├── evaluate.score.Rd │ │ ├── fisher.burden.test.Rd │ │ ├── fisher.burden.test.single.Rd │ │ ├── fit.exp.decay.Rd │ │ ├── format.pval.Rd │ │ ├── format.scientific.Rd │ │ ├── gene.meta.otf.Rd │ │ ├── get.cytoband.range.Rd │ │ ├── get.developmental.region_ids.Rd │ │ ├── get.gd.overlap.Rd │ │ ├── get.gene.color.byscore.Rd │ │ ├── get.hpo.color.Rd │ │ ├── get.ndd.region_ids.Rd │ │ ├── get.neuro.region_ids.Rd │ │ ├── get.quadrant.genes.Rd │ │ ├── get.sample.counts.Rd │ │ ├── get.sample.sizes.for.highlight.Rd │ │ ├── get.sig.gene.pw.params.Rd │ │ ├── inv.var.avg.Rd │ │ ├── load.bed3.Rd │ │ ├── load.cc.cnv.counts.Rd │ │ ├── load.chromhmm.colors.Rd │ │ ├── load.chromhmm.tracks.Rd │ │ ├── load.cnvs.from.region.Rd │ │ ├── load.cnvs.from.region.multi.Rd │ │ ├── load.credsets.Rd │ │ ├── load.dnms.Rd │ │ ├── load.feature.bed.for.highlight.Rd │ │ ├── load.features.Rd │ │ ├── load.gene.associations.Rd │ │ ├── load.gene.feature.metadata.Rd │ │ ├── load.gene.lists.Rd │ │ ├── load.gene.metadata.Rd │ │ ├── load.genelist.Rd │ │ ├── load.genes.from.gtf.Rd │ │ ├── load.hpo.jaccard.matrix.Rd │ │ ├── load.hpo.metadata.Rd │ │ ├── load.loci.Rd │ │ ├── load.manhattan.stats.Rd │ │ ├── load.meta.stats.Rd │ │ ├── load.mutrates.Rd │ │ ├── load.otf.cohort.cnvs.Rd │ │ ├── load.otf.meta.dat.Rd │ │ ├── load.other.scores.Rd │ │ ├── load.perms.bygene.Rd │ │ ├── load.pips.for.genelist.Rd │ │ ├── load.pval.matrix.Rd │ │ ├── load.rcnv.env.Rd │ │ ├── load.score.cutoffs.Rd │ │ ├── load.scores.Rd │ │ ├── load.segment.table.Rd │ │ ├── load.sumstats.for.region.Rd │ │ ├── make.meta.df.Rd │ │ ├── make.meta.lookup.table.Rd │ │ ├── merge.loci.segs.Rd │ │ ├── meta.Rd │ │ ├── meta.single.Rd │ │ ├── mod.features.Rd │ │ ├── normalize.dnms.Rd │ │ ├── or.corplot.grid.Rd │ │ ├── parse.region.for.highlight.Rd │ │ ├── perm.summary.Rd │ │ ├── pileup.cnvs.for.highlight.Rd │ │ ├── plot.all.perm.res.Rd │ │ ├── plot.bracket.Rd │ │ ├── plot.chromhmm.tracks.Rd │ │ ├── plot.cnv.key.for.highlight.Rd │ │ ├── plot.cnv.panel.for.highlight.Rd │ │ ├── plot.constraint.track.Rd │ │ ├── plot.coord.line.Rd │ │ ├── plot.dendro.Rd │ │ ├── plot.feature.bydsgroup.Rd │ │ ├── plot.features.from.bedgraph.Rd │ │ ├── plot.gene.bodies.Rd │ │ ├── plot.idio.stick.Rd │ │ ├── plot.manhattan.Rd │ │ ├── plot.na.rect.Rd │ │ ├── plot.ors.for.highlight.Rd │ │ ├── plot.pips.for.highlight.Rd │ │ ├── plot.prc.Rd │ │ ├── plot.pvalues.for.highlight.Rd │ │ ├── plot.qq.Rd │ │ ├── plot.rects.for.highlight.Rd │ │ ├── plot.roc.Rd │ │ ├── plot.seg.perms.Rd │ │ ├── plot.seg.perms.multi.Rd │ │ ├── plot.stratified.metric.Rd │ │ ├── plot.viohist.Rd │ │ ├── prc.Rd │ │ ├── prune.hpo.jaccard.matrix.Rd │ │ ├── read.assoc.stats.single.Rd │ │ ├── reorganize.perm.plots.Rd │ │ ├── robust.lm.Rd │ │ ├── roc.Rd │ │ ├── saddlepoint.adj.Rd │ │ ├── segs.scatter.Rd │ │ ├── segs.simple.vioswarm.Rd │ │ ├── segs.swarm.Rd │ │ ├── simple.legend.Rd │ │ ├── split.regions.by.effect.size.Rd │ │ ├── standardize.effect.size.Rd │ │ ├── summarize.finemapping.categories.Rd │ │ ├── superimposed.barplot.Rd │ │ └── sweeting.correction.Rd │ └── rCNV2.Rproj └── rCNV2_1.0.1.tar.gz └── utils ├── README.md ├── evenSplitter.R ├── filter_gtf_by_genelist.py ├── median.py ├── plot_manhattan_qq.R └── quantiles.py /.gitignore: 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