├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── InterMineR.Rproj ├── LICENSE ├── NAMESPACE ├── NEWS ├── R ├── InterMineR-class.R ├── InterMineR-methods.R ├── InterMineR.R ├── InterMineR_Query2XML.R ├── ListManager-class.R ├── ListManager-methods.R ├── convertToGRanges.R ├── convertToRangedSummarizedExperiment.R ├── getDatasets.R ├── getGeneIds.R ├── getIds.R ├── getWidgets.R ├── listDatasets.R ├── queries.R ├── runQuery.R ├── setConstraints.R ├── setQuery.R ├── simplifyResult.R ├── summary.R ├── webservice-class.R └── webservice-methods.R ├── README.md ├── data-raw ├── PL_DiabetesGenes.R ├── PL_DiabetesGenes.csv ├── PL_FlyTF_site_specific_TFs.R └── PL_FlyTF_site_specific_TFs.csv ├── data ├── PL_DiabetesGenes.rdata └── PL_FlyTF_site_specific_TFs.rdata ├── inst └── CITATION ├── man ├── InterMineR-class.Rd ├── InterMineR-methods.Rd ├── InterMineR-package.Rd ├── ListManager-class.Rd ├── ListManager-methods.Rd ├── PL_DiabetesGenes.Rd ├── PL_FlyTF_site_specific_TFs.Rd ├── convertToGRanges.Rd ├── convertToGeneAnswers.Rd ├── convertToRangedSummarizedExperiment.Rd ├── doEnrichment.Rd ├── getDatasets.Rd ├── getGeneIds.Rd ├── getModel.Rd ├── getRelease.Rd ├── getTemplateQuery.Rd ├── getTemplates.Rd ├── getVersion.Rd ├── getWidgets.Rd ├── initInterMine.Rd ├── listDatasets.Rd ├── listMines.Rd ├── list_manager.Rd ├── newQuery.Rd ├── runQuery.Rd ├── setConstraints.Rd ├── setQuery.Rd ├── simplifyResult.Rd ├── summary.Rd └── webservice-class.Rd └── vignettes ├── InterMineR.Rmd ├── eve_gviz.jpeg ├── export_xml.jpg ├── geneanswers_barplot.jpeg ├── geneanswers_concept_gene_network.jpg ├── geneanswers_concept_gene_network_colors.jpg ├── geneanswers_gene_interactions_network.jpg ├── geneanswers_go_structure_network.jpg ├── geneanswers_piechart.jpeg ├── geneanswers_pubs_barplot.jpeg ├── geneanswers_pubs_concept_gene_network.jpg ├── geneanswers_pubs_gene_interactions_network.jpg ├── geneanswers_pubs_piechart.jpeg ├── model.jpg ├── querybuilder.jpg ├── r_gviz.jpeg ├── 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