├── Dockerfile ├── LICENSE.txt ├── README.md ├── coding_enrichment.py ├── example_data ├── annotation_files │ ├── ucsc.refFlat.20170829.no_chrMY.gtf.gz │ └── ucsc.refFlat.20170829.promoters_up2kb_downUTR.no_chrMY.bed ├── covariates │ ├── ucsc.refFlat.20170829.no_chrMY.covariate_weights.txt │ ├── ucsc.refFlat.20170829.no_chrMY.covariates.txt │ ├── ucsc.refFlat.20170829.promoters_up2kb_downUTR.no_chrMY.base_repTime.covariate_weights.txt │ └── ucsc.refFlat.20170829.promoters_up2kb_downUTR.no_chrMY.base_repTime.covariates.txt ├── nonsilent_terms.txt ├── precomputed_apcluster │ ├── coding.ucsc.refFlat.20170829.no_chrMY │ │ └── all_genes │ │ │ └── ALL │ │ │ ├── clusters.txt │ │ │ ├── idx.txt │ │ │ └── summary.txt │ └── noncoding.ucsc.refFlat.20170829.promoters_up2kb_downUTR.no_chrMY │ │ └── apcluster_regions │ │ ├── chr1 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr10 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr11 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr12 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr13 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr14 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr15 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr16 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr17 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr18 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr19 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr2 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr20 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr21 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr22 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr3 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr4 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr5 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr6 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr7 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr8 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ ├── chr9 │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt │ │ └── chrX │ │ ├── clusters.txt │ │ ├── idx.txt │ │ └── summary.txt ├── quickstart_commands.txt ├── vcf_files.txt └── vcfs │ ├── sample_1.vcf.gz │ ├── sample_1.vcf.gz.tbi │ ├── sample_10.vcf.gz │ ├── sample_10.vcf.gz.tbi │ ├── sample_100.vcf.gz │ ├── sample_100.vcf.gz.tbi │ ├── sample_11.vcf.gz │ ├── sample_11.vcf.gz.tbi │ ├── sample_12.vcf.gz │ ├── sample_12.vcf.gz.tbi │ ├── sample_13.vcf.gz │ ├── sample_13.vcf.gz.tbi │ ├── sample_14.vcf.gz │ ├── sample_14.vcf.gz.tbi │ ├── sample_15.vcf.gz │ ├── sample_15.vcf.gz.tbi │ ├── sample_16.vcf.gz │ ├── sample_16.vcf.gz.tbi │ ├── sample_17.vcf.gz │ ├── sample_17.vcf.gz.tbi │ ├── sample_18.vcf.gz │ ├── sample_18.vcf.gz.tbi │ ├── sample_19.vcf.gz │ ├── sample_19.vcf.gz.tbi │ ├── sample_2.vcf.gz │ ├── sample_2.vcf.gz.tbi │ ├── sample_20.vcf.gz │ ├── sample_20.vcf.gz.tbi │ ├── sample_21.vcf.gz │ ├── sample_21.vcf.gz.tbi │ ├── sample_22.vcf.gz │ ├── sample_22.vcf.gz.tbi │ ├── sample_23.vcf.gz │ ├── sample_23.vcf.gz.tbi │ ├── sample_24.vcf.gz │ ├── sample_24.vcf.gz.tbi │ ├── sample_25.vcf.gz │ ├── sample_25.vcf.gz.tbi │ ├── sample_26.vcf.gz │ ├── sample_26.vcf.gz.tbi │ ├── sample_27.vcf.gz │ ├── sample_27.vcf.gz.tbi │ ├── sample_28.vcf.gz │ ├── sample_28.vcf.gz.tbi │ ├── sample_29.vcf.gz │ ├── sample_29.vcf.gz.tbi │ ├── sample_3.vcf.gz │ ├── sample_3.vcf.gz.tbi │ ├── sample_30.vcf.gz │ ├── sample_30.vcf.gz.tbi │ ├── sample_31.vcf.gz │ ├── sample_31.vcf.gz.tbi │ ├── sample_32.vcf.gz │ ├── sample_32.vcf.gz.tbi │ ├── sample_33.vcf.gz │ ├── sample_33.vcf.gz.tbi │ ├── sample_34.vcf.gz │ ├── sample_34.vcf.gz.tbi │ ├── sample_35.vcf.gz │ ├── sample_35.vcf.gz.tbi │ ├── sample_36.vcf.gz │ ├── sample_36.vcf.gz.tbi │ ├── sample_37.vcf.gz │ ├── sample_37.vcf.gz.tbi │ ├── sample_38.vcf.gz │ ├── sample_38.vcf.gz.tbi │ ├── sample_39.vcf.gz │ ├── sample_39.vcf.gz.tbi │ ├── sample_4.vcf.gz │ ├── sample_4.vcf.gz.tbi │ ├── sample_40.vcf.gz │ ├── sample_40.vcf.gz.tbi │ ├── sample_41.vcf.gz │ ├── sample_41.vcf.gz.tbi │ ├── sample_42.vcf.gz │ ├── sample_42.vcf.gz.tbi │ ├── sample_43.vcf.gz │ ├── sample_43.vcf.gz.tbi │ ├── sample_44.vcf.gz │ ├── sample_44.vcf.gz.tbi │ ├── sample_45.vcf.gz │ ├── sample_45.vcf.gz.tbi │ ├── sample_46.vcf.gz │ ├── sample_46.vcf.gz.tbi │ ├── sample_47.vcf.gz │ ├── sample_47.vcf.gz.tbi │ ├── sample_48.vcf.gz │ ├── sample_48.vcf.gz.tbi │ ├── sample_49.vcf.gz │ ├── sample_49.vcf.gz.tbi │ ├── sample_5.vcf.gz │ ├── sample_5.vcf.gz.tbi │ ├── sample_50.vcf.gz │ ├── sample_50.vcf.gz.tbi │ ├── sample_51.vcf.gz │ ├── sample_51.vcf.gz.tbi │ ├── sample_52.vcf.gz │ ├── sample_52.vcf.gz.tbi │ ├── sample_53.vcf.gz │ ├── sample_53.vcf.gz.tbi │ ├── sample_54.vcf.gz │ ├── sample_54.vcf.gz.tbi │ ├── sample_55.vcf.gz │ ├── sample_55.vcf.gz.tbi │ ├── sample_56.vcf.gz │ ├── sample_56.vcf.gz.tbi │ ├── sample_57.vcf.gz │ ├── sample_57.vcf.gz.tbi │ ├── sample_58.vcf.gz │ ├── sample_58.vcf.gz.tbi │ ├── sample_59.vcf.gz │ ├── sample_59.vcf.gz.tbi │ ├── sample_6.vcf.gz │ ├── sample_6.vcf.gz.tbi │ ├── sample_60.vcf.gz │ ├── sample_60.vcf.gz.tbi │ ├── sample_61.vcf.gz │ ├── sample_61.vcf.gz.tbi │ ├── sample_62.vcf.gz │ ├── sample_62.vcf.gz.tbi │ ├── sample_63.vcf.gz │ ├── sample_63.vcf.gz.tbi │ ├── sample_64.vcf.gz │ ├── sample_64.vcf.gz.tbi │ ├── sample_65.vcf.gz │ ├── sample_65.vcf.gz.tbi │ ├── sample_66.vcf.gz │ ├── sample_66.vcf.gz.tbi │ ├── sample_67.vcf.gz │ ├── sample_67.vcf.gz.tbi │ ├── sample_68.vcf.gz │ ├── sample_68.vcf.gz.tbi │ ├── sample_69.vcf.gz │ ├── sample_69.vcf.gz.tbi │ ├── sample_7.vcf.gz │ ├── sample_7.vcf.gz.tbi │ ├── sample_70.vcf.gz │ ├── sample_70.vcf.gz.tbi │ ├── sample_71.vcf.gz │ ├── sample_71.vcf.gz.tbi │ ├── sample_72.vcf.gz │ ├── sample_72.vcf.gz.tbi │ ├── sample_73.vcf.gz │ ├── sample_73.vcf.gz.tbi │ ├── sample_74.vcf.gz │ ├── sample_74.vcf.gz.tbi │ ├── sample_75.vcf.gz │ ├── sample_75.vcf.gz.tbi │ ├── sample_76.vcf.gz │ ├── sample_76.vcf.gz.tbi │ ├── sample_77.vcf.gz │ ├── sample_77.vcf.gz.tbi │ ├── sample_78.vcf.gz │ ├── sample_78.vcf.gz.tbi │ ├── sample_79.vcf.gz │ ├── sample_79.vcf.gz.tbi │ ├── sample_8.vcf.gz │ ├── sample_8.vcf.gz.tbi │ ├── sample_80.vcf.gz │ ├── sample_80.vcf.gz.tbi │ ├── sample_81.vcf.gz │ ├── sample_81.vcf.gz.tbi │ ├── sample_82.vcf.gz │ ├── sample_82.vcf.gz.tbi │ ├── sample_83.vcf.gz │ ├── sample_83.vcf.gz.tbi │ ├── sample_84.vcf.gz │ ├── sample_84.vcf.gz.tbi │ ├── sample_85.vcf.gz │ ├── sample_85.vcf.gz.tbi │ ├── sample_86.vcf.gz │ ├── sample_86.vcf.gz.tbi │ ├── sample_87.vcf.gz │ ├── sample_87.vcf.gz.tbi │ ├── sample_88.vcf.gz │ ├── sample_88.vcf.gz.tbi │ ├── sample_89.vcf.gz │ ├── sample_89.vcf.gz.tbi │ ├── sample_9.vcf.gz │ ├── sample_9.vcf.gz.tbi │ ├── sample_90.vcf.gz │ ├── sample_90.vcf.gz.tbi │ ├── sample_91.vcf.gz │ ├── sample_91.vcf.gz.tbi │ ├── sample_92.vcf.gz │ ├── sample_92.vcf.gz.tbi │ ├── sample_93.vcf.gz │ ├── sample_93.vcf.gz.tbi │ ├── sample_94.vcf.gz │ ├── sample_94.vcf.gz.tbi │ ├── sample_95.vcf.gz │ ├── sample_95.vcf.gz.tbi │ ├── sample_96.vcf.gz │ ├── sample_96.vcf.gz.tbi │ ├── sample_97.vcf.gz │ ├── sample_97.vcf.gz.tbi │ ├── sample_98.vcf.gz │ ├── sample_98.vcf.gz.tbi │ ├── sample_99.vcf.gz │ └── sample_99.vcf.gz.tbi ├── gene_covariate_clustering.py ├── images └── MutEnricher_Fig1_20190422_for_GitHub.png ├── math_funcs ├── math_funcs.pyx └── setup.py ├── mutEnricher.py ├── noncoding_enrichment.py ├── region_covariate_clustering.py └── utilities ├── get_gene_covariates.py └── get_region_covariates.py /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/asoltis/MutEnricher/HEAD/Dockerfile 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