├── README.md ├── documents ├── oxfj_bioinf2018_hong │ └── slide_figures │ │ ├── divine_logo_small.PNG │ │ └── divine_v0.7.png └── tutorial │ ├── divine_tutorial.md │ ├── images │ ├── divine_workflow2.png │ ├── divine_workflow_in_detail.tif │ ├── divine_xls.PNG │ ├── input_hpo_result.png │ └── mseqdr_description_input.png │ └── instruction_ccf_lri.md ├── gcn ├── __init__.py ├── bin │ ├── __init__.py │ ├── annotpipe.py │ ├── getRefTx │ │ └── get_latest_genePredExt.py │ ├── gosim │ │ ├── app_build_go.py │ │ ├── lib_geneontology.py │ │ └── mkgeneontology.py │ ├── hgConvert │ │ ├── __init__.py │ │ ├── chainData │ │ │ ├── hg18ToHg19.over.chain.gz │ │ │ └── hg19ToHg18.over.chain.gz │ │ ├── converter.py │ │ ├── hgvs_resource.py │ │ └── liftOver_exe │ │ │ └── liftOver │ ├── mkclnsnpdb.py │ ├── mkmirna.py │ ├── mkmrna.py │ ├── mknsfpdb.py │ ├── mkomim.py │ ├── mkrefgene.py │ ├── mkregulomedb.py │ ├── mksnpdb.py │ ├── mksplicedb.py │ ├── mkutrdb.py │ ├── parseutr.py │ ├── prioritize │ │ ├── __init__.py │ │ ├── bipartite_diffusion.py │ │ ├── damaging_model.py │ │ ├── divine.py │ │ ├── divine_inc.py │ │ ├── examples │ │ │ ├── runme_angelman.sh │ │ │ ├── runme_millerSyndrome.sh │ │ │ ├── runme_pfeisffer.sh │ │ │ └── runme_pfeisffer_noHpo.sh │ │ ├── lib_disease.py │ │ └── pagerank.py │ ├── rank_diseases │ │ └── build_adjm_disease_phenotypes.py │ └── setup.py ├── config │ ├── __init__.py │ ├── divine.conf │ ├── filter_tr_benign.conf │ ├── filter_tr_pathogenic.conf │ ├── filter_training_conf.txt │ ├── filterconf.txt │ ├── filterconf_dp10.txt │ ├── filterconf_hongBioInf2016.txt │ ├── filterconf_noHGMD.txt │ ├── filterconf_pass.txt │ └── lib_config.py ├── data │ ├── __init__.py │ ├── aatrans.py │ ├── codontable.py │ ├── complement.py │ ├── cut.py │ ├── data_links.txt │ ├── ese_human.py │ ├── ess_human.py │ └── pseudoautosomal_genes.py ├── etc │ ├── __init__.py │ ├── dbconfig.py │ ├── fileconfig.py │ ├── pep8.py │ └── progconfig.py └── lib │ ├── __init__.py │ ├── databases │ ├── __init__.py │ ├── annotate_clinvar_vcf.py │ ├── annotator_to_db.py │ ├── clnphe.py │ ├── geneontology.py │ ├── kegg_pathway.py │ ├── lib_disgenet.py │ ├── lib_hpo.py │ ├── lib_mysql.py │ ├── mirna.py │ ├── nsfp.py │ ├── omim.py │ ├── ready2upload │ │ ├── __init__.py │ │ ├── app_clinvitae.py │ │ ├── hgmd_table_to_vcf.py │ │ ├── integrate_disgnet.py │ │ ├── interpro_region.py │ │ ├── lib_clinvar.py │ │ ├── lib_clinvitae.py │ │ ├── lib_hgmd.py │ │ ├── reformat_cosmic.py │ │ ├── training_cadd_cli.py │ │ └── update_diseases_to_genes.py │ ├── refgene.py │ ├── refmrna.py │ ├── regulomedb.py │ ├── snpdb.py │ ├── splicedb.py │ └── utr.py │ ├── dtypes │ ├── __init__.py │ └── bunch.py │ ├── io │ ├── __init__.py │ ├── anyopen.py │ ├── bed.py │ ├── db.py │ ├── entrystream.py │ ├── fasta.py │ ├── fileutils.py │ ├── setproxy.py │ ├── vcf.py │ └── vcfutils.py │ ├── utils │ ├── __init__.py │ ├── fileutils.py │ ├── filter.py │ ├── filter_cj.py │ ├── lib_hposim.py │ ├── lib_ped.py │ ├── lib_utils.py │ └── phase.py │ └── varann │ ├── __init__.py │ ├── utils │ ├── __init__.py │ ├── fpvariants.py │ ├── gene_pmrph.py │ └── genemap.py │ └── vartype │ ├── __init__.py │ └── varant │ ├── __init__.py │ ├── annotateGerp.py │ ├── annotateLCR.py │ ├── annotateMutation.py │ ├── annotateNimblegenCap.py │ ├── annotateRegion.py │ ├── annotateSequence.py │ ├── annotator.py │ ├── varant_parser.py │ ├── vcf2xls.py │ ├── vcf2xls_varant.py │ └── vcf_mask.py ├── requirements.txt ├── resource └── support_pkg_urls.txt └── setup.py /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hwanglab/divine/HEAD/README.md -------------------------------------------------------------------------------- /documents/oxfj_bioinf2018_hong/slide_figures/divine_logo_small.PNG: -------------------------------------------------------------------------------- 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