├── README.md ├── RIVER ├── compute_scores.m ├── extract_features_byInd.m ├── extract_rvsites_ByInd.py ├── extract_scores_combined.py ├── gencode.v19.genes.v6p.patched_contigs.autosome.coding_linkRNA.gtf ├── gene_ensembl_ids.txt ├── generate_annotations_matlab.m ├── generate_data_RIVER.m ├── generate_expmat_44tissues.m ├── generate_regions.m ├── standardize.m └── tissue_names.txt ├── call_outliers ├── call_outliers_medz.R ├── call_outliers_medz_peerless.R ├── call_outliers_single_tissue.py ├── compare_single_multi_tissue_outliers.R ├── multi_tissue_replication.R └── single_tissue_replication.R ├── crispr ├── add.major.minor.alleles.py ├── crispr.bwa.aln.sort.sh ├── crispr.control.cdna.ref.fa ├── crispr.control.gdna.ref.fa ├── crispr.outlier.cdna.ref.fa ├── crispr.outlier.gdna.ref.fa ├── prioritize.for.crispr.R ├── process.crispr.donor.seq.py ├── prune.crispr.variants.R └── summarize.crispr.results.R ├── feature_construction ├── 20130606_sample_info.txt ├── ER_pipeline.sh ├── TFBS_pipeline.sh ├── add_features_variant_beds.sh ├── assess.euro.subpop.R ├── build_count_summaries_all_genes.sh ├── build_feature_set.py ├── build_feature_summaries_all_genes.sh ├── calc.uk10k.freqs.sh ├── calculate.euro.subpop.af.sh ├── compileCADDscores.sh ├── compile_features_outliers.sh ├── compile_features_outliers_nothresh.sh ├── compile_features_outliers_peerless.sh ├── compile_features_outliers_singletissue.sh ├── er.tissues.map.grouped.tsv ├── extract.1kg.AF.sh ├── extractCADDscores_ekt.py ├── pick_outliers_controls_imbalanced.py ├── pouya.raw.summary.py ├── process.1kg.AF.py ├── run_add_features_variant_beds.sh ├── run_build_feature_count_summaries_all_genes.sh ├── run_compile_features_outliers.sh ├── run_compile_features_outliers_peerless.sh ├── subset.CADD.features.sh ├── vcf2bedfiles.sh ├── vcf2bedfiles_helper_processVCF.sh ├── vcf2bedfiles_helper_processVCF_SV.sh ├── vcf2bedfiles_helper_processVCFtoolsOutput.sh └── vcf2bedfiles_helper_processVCFtoolsOutput_CNV.sh ├── paper_figures ├── EDF10bd.R ├── EDF10ef.Zscores.R ├── EDF10ef.rpkm.R ├── EDF7.R ├── EDF9c.R ├── EDF9d.R ├── EDF9e.R ├── Generate_figures_RIVER_VaryingThrds.R ├── annotate.variants.by.gene.sh ├── count_rarevars.sh ├── enrichment.functions.R ├── figure1a.plot.cartoon.example.R ├── figure1b.outlier.sharing.R ├── figure1c.replication.rate.consistent.R ├── figure2.R ├── figure2a.count.enrichments.R ├── figure2b.threshold.enrichments.R ├── figure2c.ASE.enrichments.R ├── figure3.R ├── figure3a.rare.variant.class.enrichments.R ├── figure3b.feature.enrichments.R ├── figure3de.outlier.effect.size.R ├── figure4.R ├── figure4a.uk10k.R ├── figure4b.exac.enrichments.R ├── figure4c.gene.list.enrichments.R ├── figure5b.R ├── figure5c.R ├── getPlots.R ├── gtex_tissue_colors.txt ├── main_RIVER_10CV.R ├── main_RIVER_VaryingThrds.R ├── muscle_covariates_peerfactors.R ├── pick.cartoon.example.sh ├── process_results.R ├── pve_samples_pertiss.R ├── pve_subject_pertiss.R ├── superheat_expression.R ├── superheat_peer_muscle.R ├── suppfig.count.enrichments.R ├── suppfig.egene.enrichment.R ├── suppfig.number.outliers.per.individual.R ├── suppfig.number.rare.vars.pca.R ├── suppfig.over.under.expression.R ├── suppfig.rare.var.counts.disease.genes.gtex.cohort.R └── suppfig.single.replication.compare.multi.R ├── preprocessing ├── PEER │ ├── PEER.pipeline.sh │ ├── calc.PEER.factors.all.tissues.sh │ ├── calc.PEER.factors.core.R │ ├── calc.PEER.factors.single.tissue.sh │ ├── calc.residuals.core.R │ ├── calc.residuals.sh │ ├── calc_residuals_covs_peerless.R │ ├── calc_residuals_covs_peerless.sh │ ├── gtex_eqtl_tissues.txt │ └── preprocess.expr.data.R ├── gather_filter_normalized_expression.py ├── gather_filter_normalized_expression_peerless.py ├── gather_filter_rpkm.py ├── get_median_rpkms.R ├── get_tissue_by_individual.sh ├── gtex_2015-01-12_AF_ids.txt ├── gtex_2015-01-12_wgs_ids.148.txt ├── gtex_2015-01-12_wgs_ids.txt ├── gtex_2015-01-12_wgs_ids_HallLabSV.txt ├── gtf2TSS.sh ├── 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