├── .github ├── ISSUE_TEMPLATE │ ├── bug_report.yml │ ├── doc_improvement.yml │ ├── feature_request.yml │ └── question.yml └── workflows │ └── workflow.yml ├── .gitignore ├── .travis.yml ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── docs ├── Makefile ├── _templates │ ├── module.rst │ └── package.rst ├── conf.py ├── cuna.rst ├── data │ ├── CuNA_network_tcga_breastcancer.xlsx │ ├── TCGA_Rank_score_nodes.txt │ ├── cunaviz_False_25.html │ ├── cunaviz_False_50.html │ ├── cunaviz_True_25.html │ ├── cunaviz_True_50.html │ ├── cunaviz_demo.html │ ├── tcga_communities.csv │ ├── tcga_mixomics_new_train_forcuna.csv │ └── tcga_subtypes_train.csv ├── delta.rst ├── img │ ├── CuNA_pipeline.png │ ├── Geno4SD.png │ ├── LSMWorkflow.png │ ├── cunaverse.png │ ├── reveal_flowchart.jpeg │ ├── rubricOE_logo.png │ └── rubricoeflowchart.png ├── index.rst ├── lsm.rst ├── reveal.rst ├── rubricoe.rst └── source │ ├── installation.md │ ├── modules.rst │ ├── overview.md │ └── tutorial.md ├── geno4sd ├── __init__.py ├── evolution │ ├── Delta │ │ ├── README.md │ │ ├── __init__.py │ │ └── delta.py │ └── __init__.py ├── liquid_biopsy │ ├── LSM │ │ ├── LSM.py │ │ ├── README.md │ │ ├── _LSMFunctions.py │ │ └── __init__.py │ └── __init__.py ├── ml_tools │ ├── README.md │ ├── ReVeaL.py │ ├── __init__.py │ └── rubricoe │ │ ├── __init__.py │ │ ├── feature_ranking.py │ │ ├── helper_funcs.py │ │ ├── lreb.py │ │ └── rubricoe.py ├── statgen │ ├── GWAS │ │ ├── GWAS.py │ │ ├── QC.py │ │ ├── QCandGWAS.sh │ │ └── README.md │ ├── README.md │ ├── __init__.py │ └── masklmm │ │ └── MaSkLMM.py ├── topology │ ├── CuNA │ │ ├── cumulants.jl │ │ ├── cumulants.py │ │ ├── cuna.py │ │ ├── cures.py │ │ ├── julia-cumulants-readme.txt │ │ └── merged-data-filtered-trancripts.tsv │ ├── README.md │ └── __init__.py ├── utils │ ├── __init__.py │ ├── clustering_tools.py │ ├── log_odds.py │ ├── read_genesets.py │ ├── read_plink.py │ ├── scRNA.py │ ├── snpEff │ │ ├── LICENSE.md │ │ ├── SnpSift.jar │ │ ├── __init__.py │ │ ├── examples │ │ │ ├── 1kg.head_chr1.filtered.vcf.gz │ │ │ ├── 1kg.head_chr1.vcf.gz │ │ │ ├── cancer.ann.vcf │ │ │ ├── cancer.eff.vcf │ │ │ ├── cancer.vcf │ │ │ ├── cancer_pedigree.ann.vcf │ │ │ ├── cancer_pedigree.vcf │ │ │ ├── example_motif.vcf │ │ │ ├── examples.sh │ │ │ ├── file.vcf │ │ │ ├── intervals.bed │ │ │ ├── my_annotations.bed │ │ │ ├── samples_cancer.txt │ │ │ ├── samples_cancer_one.txt │ │ │ ├── test.1KG.ann_encode.vcf │ │ │ ├── test.1KG.ann_reg.vcf │ │ │ ├── test.1KG.vcf │ │ │ ├── test.ann.vcf │ │ │ ├── test.chr22.ann.filter_missense.vcf │ │ │ ├── test.chr22.ann.filter_missense_any.vcf │ │ │ ├── test.chr22.ann.filter_missense_any_TRMT2A.vcf │ │ │ ├── test.chr22.ann.filter_missense_first.vcf │ │ │ ├── test.chr22.ann.one_per_line.txt │ │ │ ├── test.chr22.ann.txt │ │ │ ├── test.chr22.ann.vcf │ │ │ ├── test.chr22.vcf │ │ │ ├── test.vcf │ │ │ ├── variants_1.ann.vcf │ │ │ ├── variants_1.vcf │ │ │ ├── variants_2.ann.vcf │ │ │ └── variants_2.vcf │ │ ├── exec │ │ │ ├── snpeff │ │ │ └── snpsift │ │ ├── galaxy │ │ │ ├── snpEff.xml │ │ │ ├── snpEffWrapper.pl │ │ │ ├── snpEff_download.xml │ │ │ ├── snpSiftWrapper.pl │ │ │ ├── snpSift_annotate.xml │ │ │ ├── snpSift_caseControl.xml │ │ │ ├── snpSift_filter.xml │ │ │ ├── snpSift_int.xml │ │ │ ├── tool-data │ │ │ │ ├── snpEff_genomes.loc │ │ │ │ └── snpEff_genomes.loc.sample │ │ │ ├── tool_conf.xml │ │ │ └── tool_dependencies.xml │ │ ├── scripts │ │ │ ├── 1kg.sh │ │ │ ├── annotate_demo.sh │ │ │ ├── annotate_demo_GATK.sh │ │ │ ├── bedEffOnePerLine.pl │ │ │ ├── buildDbNcbi.sh │ │ │ ├── cgShore.pl │ │ │ ├── cgShore.sh │ │ │ ├── countColumns.py │ │ │ ├── db.pl │ │ │ ├── extractSequences.pl │ │ │ ├── fasta2tab.pl │ │ │ ├── fastaSample.pl │ │ │ ├── fastaSplit.pl │ │ │ ├── fastqSplit.pl │ │ │ ├── filterBy.py │ │ │ ├── gffRemovePhase.pl │ │ │ ├── gsa │ │ │ │ ├── bayesFactor_correction_scoreCount.r │ │ │ │ ├── bayesFactor_correction_scoreCount.sh │ │ │ │ ├── bayesFactor_correction_scoreCount_max10.sh │ │ │ │ ├── checkGeneNames.py │ │ │ │ ├── create_sets.bds │ │ │ │ ├── geneSetOverlap.py │ │ │ │ ├── geneSetOverlap.sort.txt │ │ │ │ ├── geneSetsGtex.py │ │ │ │ ├── pvalue_correction_scoreCount.r │ │ │ │ ├── pvalue_correction_scoreCount.sh │ │ │ │ └── pvalue_correction_scoreCount_min10.sh │ │ │ ├── isutf8.py │ │ │ ├── join.pl │ │ │ ├── joinSnpEff.pl │ │ │ ├── make_and_commit_docs.sh │ │ │ ├── make_dbNSFP.sh │ │ │ ├── nextProt_filter.pl │ │ │ ├── ped2vcf.py │ │ │ ├── plot.pl │ │ │ ├── plotHistogram.pl │ │ │ ├── plotLabel.pl │ │ │ ├── plotMA.pl │ │ │ ├── plotQQ.pl │ │ │ ├── plotQQsubsample.pl │ │ │ ├── plotSmoothScatter.pl │ │ │ ├── plotXY.pl │ │ │ ├── queue.pl │ │ │ ├── sam2fastq.pl │ │ │ ├── sample.pl │ │ │ ├── snpEff │ │ │ ├── snpSift │ │ │ ├── snpSift_filter_sample_to_number.pl │ │ │ ├── sortLine.py │ │ │ ├── splitChr.pl │ │ │ ├── statsNum.pl │ │ │ ├── swapCols.pl │ │ │ ├── transpose.pl │ │ │ ├── txt2fa.pl │ │ │ ├── txt2vcf.py │ │ │ ├── uniqCount.pl │ │ │ ├── uniqCut.pl │ │ │ ├── vcfAnnFirst.py │ │ │ ├── vcfBareBones.pl │ │ │ ├── vcfEffHighest.ORI.py │ │ │ ├── vcfEffOnePerLine.pl │ │ │ ├── vcfFilterSamples.pl │ │ │ ├── vcfInfoOnePerLine.pl │ │ │ ├── vcfOnlyAlts.pl │ │ │ ├── vcfReduceGenotypes.pl │ │ │ ├── vcfRefCorrect.py │ │ │ └── wigSplit.pl │ │ ├── snpEff.config │ │ └── snpEff.jar │ └── snpeff_tools.py └── version.py ├── requirements.txt ├── sample_data ├── CuNA_MockData.csv ├── CuNA_TCGA_sample_data.csv ├── LSM_MafData.csv ├── LSM_sampleData.csv ├── bn_causal_idx ├── bn_cov ├── bn_pheno ├── bn_simdata.bed ├── bn_simdata.bim ├── bn_simdata.fam ├── parameters_Sim_Test.txt ├── parameters_Test.txt └── parameters_Test_Multi.txt ├── tests ├── __init__.py ├── test_ReVeaL.py └── test_delta.py └── tutorials ├── CuNA.ipynb ├── Delta_tutorial.ipynb ├── LSM_tutorial.ipynb ├── MaSkLMM_tutorial.ipynb ├── ReVeaL.ipynb ├── RubricOE.ipynb ├── StatGen.ipynb └── readme.md /.github/ISSUE_TEMPLATE/bug_report.yml: 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