LICENSE
MANIFEST.in
README.md
master-test.sh
requirements.txt
setup.py
docs/EXAMPLES.rst
docs/Makefile
docs/TODO.rst
docs/build.sh
docs/conf.py
docs/gemini.ai
docs/gemini.png
docs/index.rst
docs/requirements.txt
docs/_static/labibi.css
docs/_static/labibi.js
docs/content/acknowledgements.rst
docs/content/api.rst
docs/content/browser.rst
docs/content/caveats.rst
docs/content/database_schema.rst
docs/content/faq.rst
docs/content/functional_annotation.rst
docs/content/genotype_query_engines.rst
docs/content/history.rst
docs/content/installation.rst
docs/content/other.rst
docs/content/preprocessing.rst
docs/content/querying.rst
docs/content/quick_start.rst
docs/content/tools.rst
docs/images/browser-query.png
docs/images/gene_wise_example.png
docs/images/overview.png
docs/images/query-speed.png
docs/templates/layout.html
docs/templates/page.html
docs/templates/sidebar-intro.html
docs/themes/rtd/theme.conf
docs/themes/rtd/static/rtd.css_t
gemini/GeminiQuery.py
gemini/__init__.py
gemini/anno_info.py
gemini/annotations.py
gemini/compression.py
gemini/config.py
gemini/database.py
gemini/dgidb.py
gemini/gemini_actionable_mutations.py
gemini/gemini_amend.py
gemini/gemini_annotate.py
gemini/gemini_bcolz.py
gemini/gemini_browser.py
gemini/gemini_constants.py
gemini/gemini_dbinfo.py
gemini/gemini_dump.py
gemini/gemini_load.py
gemini/gemini_load_chunk.py
gemini/gemini_load_chunk2.py
gemini/gemini_main.py
gemini/gemini_merge_chunks.py
gemini/gemini_plot.py
gemini/gemini_query.py
gemini/gemini_region.py
gemini/gemini_set_somatic.py
gemini/gemini_stats.py
gemini/gemini_subjects.py
gemini/gemini_update.py
gemini/gemini_utils.py
gemini/gemini_windower.py
gemini/gene_table.py
gemini/genewise.py
gemini/gim.py
gemini/infotag.py
gemini/install-data.py
gemini/mendelianerror.py
gemini/pdict.py
gemini/ped.py
gemini/popgen.py
gemini/sql.py
gemini/sql_extended.py
gemini/sql_utils.py
gemini/stats.py
gemini/structural_variants.py
gemini/tool_burden_tests.py
gemini/tool_fusions.py
gemini/tool_homozygosity_runs.py
gemini/tool_interactions.py
gemini/tool_lof_sieve.py
gemini/tool_pathways.py
gemini/tool_qc.py
gemini/version.py
gemini.egg-info/PKG-INFO
gemini.egg-info/SOURCES.txt
gemini.egg-info/dependency_links.txt
gemini.egg-info/not-zip-safe
gemini.egg-info/requires.txt
gemini.egg-info/top_level.txt
gemini/annotation_provenance/clinvar.py
gemini/annotation_provenance/make-1000G.sh
gemini/annotation_provenance/make-29way-conservation.sh
gemini/annotation_provenance/make-cadd.sh
gemini/annotation_provenance/make-cancer-census.sh
gemini/annotation_provenance/make-clinvar.sh
gemini/annotation_provenance/make-cosmic.sh
gemini/annotation_provenance/make-cse.sh
gemini/annotation_provenance/make-dbsnp.sh
gemini/annotation_provenance/make-encode-chrom-segs.sh
gemini/annotation_provenance/make-encode-tfbs-clustering.sh
gemini/annotation_provenance/make-esp-variants.sh
gemini/annotation_provenance/make-exac.sh
gemini/annotation_provenance/make-fitcons.sh
gemini/annotation_provenance/make-geno2mp.sh
gemini/annotation_provenance/make-ncbi-grc-patches.py
gemini/annotation_provenance/make-pfam-ucsc.sh
gemini/annotation_provenance/make-recombination.sh
gemini/annotation_provenance/make-rmsk-meta.sh
gemini/annotation_provenance/make-stam-125-cells-dnase1-clusters.sh
gemini/annotation_provenance/make-vista-enhancers.sh
gemini/annotation_provenance/sanitize-esp.py
gemini/annotation_provenance/HPRD/hprd_graph.py
gemini/annotation_provenance/KEGG/KEGG_REST_files/all_kegg_hsa_to_uniprot
gemini/annotation_provenance/KEGG/KEGG_REST_files/kegg_hsa_to_gene
gemini/annotation_provenance/KEGG/KEGG_REST_files/kegg_hsa_to_path
gemini/annotation_provenance/KEGG/KEGG_REST_files/note
gemini/annotation_provenance/KEGG/KEGG_REST_files/pathways
gemini/annotation_provenance/KEGG/make_path_files/add_path
gemini/annotation_provenance/KEGG/make_path_files/ensembl_genes66
gemini/annotation_provenance/KEGG/make_path_files/format.sh
gemini/annotation_provenance/KEGG/make_path_files/kegg_hsa_to_gene_fmt
gemini/annotation_provenance/KEGG/make_path_files/kegg_pathway
gemini/annotation_provenance/KEGG/make_path_files/map_uni2hsa2gene
gemini/annotation_provenance/KEGG/make_path_files/mart_export_transcripts66.txt
gemini/annotation_provenance/KEGG/make_path_files/mart_header
gemini/annotation_provenance/KEGG/make_path_files/unihsagene.py
gemini/annotation_provenance/KEGG/make_path_files/uniprot_hsa_map
gemini/annotation_provenance/gene_table/README
gemini/annotation_provenance/gene_table/combined_gene_table.py
gemini/annotation_provenance/gene_table/ensembl.py
gemini/annotation_provenance/gene_table/map_entrez.py
gemini/annotation_provenance/gene_table/synonym.py
gemini/annotation_provenance/gene_table/anno_files/HMD_HumanPhenotype.rpt
gemini/annotation_provenance/gene_table/anno_files/genic_intolerance_dataset2
gemini/annotation_provenance/gene_table/downloads/HGNC_download
gemini/annotation_provenance/gene_table/downloads/hgnc.query.pl
gemini/annotation_provenance/gene_table/downloads/mart_export1
gemini/annotation_provenance/gene_table/downloads/mart_export2
gemini/annotation_provenance/gene_table/downloads/mart_export3
gemini/annotation_provenance/gene_table/downloads/query1.pl
gemini/annotation_provenance/gene_table/downloads/query2.pl
gemini/annotation_provenance/gene_table/downloads/query3.pl
gemini/data/__init__.py
gemini/data/gemini.conf
gemini/scripts/__init__.py
gemini/scripts/gemini
gemini/scripts/gemini_install.py
gemini/static/css/gemini.css
gemini/static/img/gemini.png
gemini/static/third_party/bootstrap/css/bootstrap-responsive.css
gemini/static/third_party/bootstrap/css/bootstrap-responsive.min.css
gemini/static/third_party/bootstrap/css/bootstrap-rowlink.css
gemini/static/third_party/bootstrap/css/bootstrap-rowlink.min.css
gemini/static/third_party/bootstrap/css/bootstrap.css
gemini/static/third_party/bootstrap/css/bootstrap.min.css
gemini/static/third_party/bootstrap/img/glyphicons-halflings-white.png
gemini/static/third_party/bootstrap/img/glyphicons-halflings.png
gemini/static/third_party/bootstrap/js/bootstrap-rowlink.js
gemini/static/third_party/bootstrap/js/bootstrap-rowlink.min.js
gemini/static/third_party/bootstrap/js/bootstrap.js
gemini/static/third_party/bootstrap/js/bootstrap.min.js
gemini/static/third_party/jquery/jquery-1.7.1.js
gemini/static/third_party/jquery-ui/jquery-ui.min.js
gemini/tests/__init__.py
gemini/views/auto_dom.j2.html
gemini/views/auto_rec.j2.html
gemini/views/base.j2.html
gemini/views/db_schema.j2.html
gemini/views/de_novo.j2.html
gemini/views/query.j2.html
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.snpEff.vcf
test/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites.snippet.vcf
test/bcolz-setup.sh
test/bcolz-test.sh
test/check.sh
test/data-setup.sh
test/drop-gl-columns.py
test/from_inheritance.ped
test/from_inheritance.vcf
test/test-amend.sh
test/test-annotate-tool-vcf.sh
test/test-annotate-tool.sh
test/test-auto-dom.sh
test/test-auto-rec.sh
test/test-bcolz.sh
test/test-burden.sh
test/test-cadd.sh
test/test-clinvar.sh
test/test-columns.sh
test/test-comphet.sh
test/test-cosmic.sh
test/test-dashes.sh
test/test-de-novo.sh
test/test-dump.sh
test/test-eff.sh
test/test-effstring.sh
test/test-encode.sh
test/test-esp.sh
test/test-exac.sh
test/test-fitcons.sh
test/test-fusions.sh
test/test-genewise.sh
test/test-geno2mp.sh
test/test-genome.sh
test/test-genotype-likelihoods.sh
test/test-genotypes.sh
test/test-gerp.sh
test/test-interactions.sh
test/test-load.sh
test/test-lofsieve.sh
test/test-map.sh
test/test-mendel-error.sh
test/test-multi-col.sh
test/test-multiple-alts.sh
test/test-no-gls.sh
test/test-pathtool.sh
test/test-pfam.sh
test/test-pop.sh
test/test-query.sh
test/test-region.sh
test/test-roh.sh
test/test-somatic.sh
test/test-stats.sh
test/test-t-all.sh
test/test-vcf-output.sh
test/test-vep-extra.sh
test/test-vep-extra.vcf
test/test-wildcards.sh
test/test-windower.sh
test/test.PLs.vcf
test/test.auto_dom.no_parents.2.ped
test/test.auto_dom.no_parents.2.vcf
test/test.auto_dom.no_parents.3.ped
test/test.auto_dom.no_parents.3.vcf
test/test.auto_dom.no_parents.4.ped
test/test.auto_dom.no_parents.4.vcf
test/test.auto_dom.no_parents.5.ped
test/test.auto_dom.no_parents.5.vcf
test/test.auto_dom.no_parents.ped
test/test.auto_dom.no_parents.vcf
test/test.auto_dom.ped
test/test.auto_dom.vcf
test/test.auto_rec.no_parents.2.ped
test/test.auto_rec.no_parents.2.vcf
test/test.auto_rec.no_parents.3.ped
test/test.auto_rec.no_parents.3.vcf
test/test.auto_rec.no_parents.4.ped
test/test.auto_rec.no_parents.4.vcf
test/test.auto_rec.no_parents.5.ped
test/test.auto_rec.no_parents.5.vcf
test/test.auto_rec.no_parents.ped
test/test.auto_rec.no_parents.vcf
test/test.auto_rec.ped
test/test.auto_rec.vcf
test/test.burden.ped
test/test.burden.vcf
test/test.cadd.vcf
test/test.clinvar.vcf
test/test.clinvar_gene_pheno.vcf
test/test.comp_het.2.ped
test/test.comp_het.2.vcf
test/test.comp_het.3.vcf
test/test.comp_het.4.vcf
test/test.comp_het.5.vcf
test/test.comp_het.6.vcf
test/test.comp_het.7.vcf
test/test.comp_het.ped
test/test.comp_het.singleton.vcf
test/test.comp_het.unphase.vcf
test/test.comp_het.vcf
test/test.cosmic.vcf
test/test.dashes.ped
test/test.dashes.vcf
test/test.de_novo.affected.and.unaffected.ped
test/test.de_novo.affected.and.unaffected.vcf
test/test.de_novo.ped
test/test.de_novo.vcf
test/test.eff.vcf
test/test.esp.zero.vcf
test/test.exac.vcf
test/test.family.vcf
test/test.fusions.ped
test/test.fusions.vcf
test/test.geno2mp.vcf
test/test.mendel.ped
test/test.mendel.vcf
test/test.multiple-alts.decomp.snpeff.vcf
test/test.passonly.vcf
test/test.query.vcf
test/test.region.vep.vcf
test/test.roh.vcf
test/test.snpeff.vcf
test/test.somatic.ped
test/test.somatic.vcf
test/test.vcf_id.snpeff.vcf
test/test1.snpeff.vcf
test/test2.snpeff.vcf
test/test3.snpeff.vcf
test/test4.snpeff.ped
test/test4.vep.snpeff.vcf
test/test5.vep.snpeff.vcf
test/test_amend2_sample.ped
test/test_amend_sample.ped
test/test_extended_ped.ped