├── .coveragerc ├── .github ├── FUNDING.yml ├── ISSUE_TEMPLATE │ ├── bug_report.md │ └── feature_request.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── lint.yml │ ├── rebase.yml │ ├── release.yml │ └── test.yml ├── .gitignore ├── .pre-commit-config.yaml ├── CHANGELOG.md ├── CODE_OF_CONDUCT.md ├── LICENSE ├── README.md ├── README.pypi ├── codecov.yml ├── doc ├── Makefile ├── _static │ ├── bioinformatics-sidebar-logo.svg │ └── custom.css ├── _templates │ ├── about.html │ ├── globaltoc.html │ └── useful_links.html ├── conf.py ├── contents.rst ├── index.rst ├── make.bat ├── scripting_reference.rst ├── scripting_references │ ├── annotation.rst │ ├── code │ │ ├── geo │ │ │ ├── dataset_info.py │ │ │ ├── dataset_samples.py │ │ │ └── predict_disease_state.py │ │ └── go │ │ │ ├── enrichment.py │ │ │ └── gene_annotations.py │ ├── dicty_phenotypes.rst │ ├── geneset.rst │ ├── geo.rst │ ├── go.rst │ ├── kegg.rst │ ├── marker_genes.rst │ ├── ncbi_gene.rst │ ├── ncbi_taxonomy.rst │ ├── resolwe.rst │ └── serverfiles.rst ├── widgets.json ├── widgets.rst └── widgets │ ├── annotate_projection.md │ ├── cluster_analysis.md │ ├── databases_update.md │ ├── dicty_express.md │ ├── differential_expression.md │ ├── gene_set_enrichment.md │ ├── gene_sets.md │ ├── genes.md │ ├── geo_data_sets.md │ ├── go_browser.md │ ├── homologs.md │ ├── icons │ ├── annotator.png │ ├── cluster-analysis.png │ ├── databases-update.png │ ├── dicty-express.png │ ├── differential-expression.png │ ├── gene-set-enrichment.png │ ├── genes.png │ ├── geo-data-sets.png │ ├── go-browser.png │ ├── kegg-pathways.png │ └── volcano-plot.png │ ├── images │ ├── annotate_projection │ │ ├── annotator-example.png │ │ ├── annotator-example2.png │ │ └── annotator-stamped.png │ ├── cluster_analysis │ │ ├── Cluster-Analysis-example.png │ │ └── Cluster-Analysis-stamped.png │ ├── database_update │ │ ├── Add-Dataset.png │ │ └── Databases-Update-stamped.png │ ├── dicty_express │ │ ├── dictyExpress-Example.png │ │ └── dictyExpress-stamped.png │ ├── differential_expression │ │ ├── Differential-Expression-Example.png │ │ └── Differential-Expression-stamped.png │ ├── gene-sets │ │ ├── Gene-Sets-example.png │ │ ├── Gene-Sets-example2.png │ │ └── Gene-Sets-stamped.png │ ├── gene_set_enrichment │ │ ├── Gene-Set-Enrichment-Example.png │ │ └── Gene-Set-Enrichment-stamped.png │ ├── genes │ │ ├── genes-Example.png │ │ └── genes-stamped.png │ ├── geo_data_sets │ │ ├── GEO-Data-Sets-Example.png │ │ └── GEO-Data-Sets-stamped.png │ ├── go_browser │ │ ├── Filter-Select.png │ │ ├── GO-Browser-Example.png │ │ └── GO-Browser-stamped.png │ ├── homologs │ │ ├── Homologs-Example.png │ │ └── Homologs-stamped.png │ ├── kegg_pathways │ │ ├── KEGG-Pathways-Example.png │ │ └── KEGG-Pathways-stamped.png │ ├── marker_genes │ │ ├── Marker-Genes-example.png │ │ └── Marker-Genes-stamped.png │ ├── single_sample_scoring │ │ ├── Single-Sample-Scoring-Example.png │ │ └── Single-Sample-Scoring-stamped.png │ └── volcano_plot │ │ ├── Volcano-Plot-Example.png │ │ └── Volcano-Plot-stamped.png │ ├── kegg_pathways.md │ ├── marker_genes.md │ ├── single_sample_scoring.md │ └── volcano_plot.md ├── orangecontrib ├── __init__.py └── bioinformatics │ ├── __init__.py │ ├── annotation │ ├── __init__.py │ ├── annotate_projection.py │ └── annotate_samples.py │ ├── cluster_analysis │ └── __init__.py │ ├── dicty │ ├── __init__.py │ └── phenotypes.py │ ├── geneset │ ├── __init__.py │ └── utils.py │ ├── geo │ ├── __init__.py │ └── dataset.py │ ├── go │ ├── __init__.py │ └── config.py │ ├── kegg │ ├── __init__.py │ ├── api.py │ ├── brite.py │ ├── caching.py │ ├── conf.py │ ├── databases.py │ ├── entry │ │ ├── __init__.py │ │ ├── fields.py │ │ └── parser.py │ ├── pathway.py │ ├── service.py │ └── types.py │ ├── ncbi │ ├── __init__.py │ ├── gene │ │ ├── __init__.py │ │ └── config.py │ ├── homologene │ │ └── __init__.py │ └── taxonomy │ │ ├── __init__.py │ │ └── utils.py │ ├── preprocess │ ├── __init__.py │ └── normalize.py │ ├── resolwe │ ├── __init__.py │ ├── genapi.py │ ├── resapi.py │ └── utils.py │ ├── tests │ ├── __init__.py │ ├── annotation │ │ ├── __init__.py │ │ ├── test_annotate_projection.py │ │ └── test_annotate_samples.py │ ├── kegg │ │ ├── __init__.py │ │ ├── test_api.py │ │ ├── test_databases.py │ │ └── test_entry.py │ ├── ncbi │ │ ├── __init__.py │ │ ├── test_gene.py │ │ ├── test_homologene.py │ │ └── test_taxonomy.py │ ├── preprocess │ │ ├── __init__.py │ │ └── test_normalize.py │ ├── resolwe │ │ ├── __init__.py │ │ └── test_genapi.py │ ├── test_geneset.py │ ├── test_geo.py │ ├── test_statistics.py │ ├── utils │ │ ├── __init__.py │ │ └── test_gui.py │ └── widgets │ │ ├── __init__.py │ │ ├── components │ │ ├── __init__.py │ │ ├── test_gene_set_selection.py │ │ └── test_resolwe.py │ │ ├── data │ │ ├── genes.tab │ │ └── markers-panglao.pkl │ │ ├── test_OWAnnotateProjection.py │ │ ├── test_OWDifferentialExpression.py │ │ ├── test_OWGEODatasets.py │ │ ├── test_OWGeneSets.py │ │ ├── test_OWGenes.py │ │ ├── test_OWGenialisExpressions.py │ │ ├── test_OWHomologs.py │ │ └── test_OWMarkerGenes.py │ ├── utils │ ├── __init__.py │ ├── serverfiles.py │ └── statistics.py │ └── widgets │ ├── OWAnnotateProjection.py │ ├── OWClusterAnalysis.py │ ├── OWDatabasesUpdate.py │ ├── OWDifferentialExpression.py │ ├── OWGEODatasets.py │ ├── OWGOBrowser.py │ ├── OWGeneSetEnrichment.py │ ├── OWGeneSets.py │ ├── OWGenes.py │ ├── OWGenialisExpressions.py │ ├── OWHomologs.py │ ├── OWKEGGPathwayBrowser.py │ ├── OWMarkerGenes.py │ ├── OWSingleSampleScoring.py │ ├── OWVolcanoPlot.py │ ├── OWdictyExpress.py │ ├── __init__.py │ ├── components │ ├── __init__.py │ ├── gene_set_selection.py │ └── resolwe.py │ ├── icons │ ├── Category-Bioinformatics.svg │ ├── OWAnnotateProjection.svg │ ├── OWClusterAnalysis.svg │ ├── OWDatabasesUpdate.svg │ ├── OWDifferentialExpression.svg │ ├── OWGEODatasets.svg │ ├── OWGOBrowser.svg │ ├── OWGeneInfo.svg │ ├── OWGeneSetEnrichment.svg │ ├── OWGeneSets.svg │ ├── 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