# -*- encoding: utf-8 -*- # stub: pets 0.2.5 ruby lib Gem::Specification.new do |s| s.name = "pets".freeze s.version = "0.2.5".freeze s.required_rubygems_version = Gem::Requirement.new(">= 0".freeze) if s.respond_to? :required_rubygems_version= s.require_paths = ["lib".freeze] s.authors = ["Elena Rojano, Pedro Seoane".freeze] s.date = "2023-08-04" s.description = "PETS suite includes three different tools. CohortAnalyzer performs the calculation of several statistics that gives an overview of a cohort of patients to analyse. Reg2Phen uses associations between pathological phenotypes and regions of the genome (these associations can be calculated from the cohort of patients if they include genotypic & phenotypic information using NetAnalyzer, another Ruby gem) to find, for a given genomic region, which pathological phenotypes have been associated with that region. The third tool, Phen2Reg, is a predictor that using the same associations as Reg2Phen, predicts which genomic regions can be the cause of a list of pathological phenotypes observed in a patient.".freeze s.email = ["elenarojano@uma.es, seoanezonjic@uma.es".freeze] s.executables = ["area_under_curve_pr.rb".freeze, "association_metrics_average.rb".freeze, "coPatReporter.rb".freeze, "comPatMondo.rb".freeze, "console".freeze, "evidence_profiler.rb".freeze, "fmeasure_index.rb".freeze, "generate_HPO_IC_table.rb".freeze, "get_PR_values.rb".freeze, "get_gen_features.rb".freeze, "get_network_nodes.rb".freeze, "get_sorted_profs.rb".freeze, "install_deps.rb".freeze, "merge_by_cluster.rb".freeze, "merge_pairs.rb".freeze, "paco_translator.rb".freeze, "phen2reg.rb".freeze, "phen2reg_predictor_check.rb".freeze, "profile_cleaner.rb".freeze, "profiles2phenopacket.rb".freeze, "reg2phen.rb".freeze, "region_to_patients_generator.rb".freeze, "relate_CI_to_association_value.rb".freeze, "setup".freeze] s.files = [".gitignore".freeze, ".rspec".freeze, ".travis.yml".freeze, "Gemfile".freeze, "LICENSE.txt".freeze, "README.md".freeze, "Rakefile".freeze, "bin/area_under_curve_pr.rb".freeze, "bin/association_metrics_average.rb".freeze, "bin/coPatReporter.rb".freeze, "bin/comPatMondo.rb".freeze, "bin/console".freeze, "bin/evidence_profiler.rb".freeze, "bin/fmeasure_index.rb".freeze, "bin/generate_HPO_IC_table.rb".freeze, "bin/get_PR_values.rb".freeze, "bin/get_gen_features.rb".freeze, "bin/get_network_nodes.rb".freeze, "bin/get_sorted_profs.rb".freeze, "bin/install_deps.rb".freeze, "bin/merge_by_cluster.rb".freeze, "bin/merge_pairs.rb".freeze, "bin/paco_translator.rb".freeze, "bin/phen2reg.rb".freeze, "bin/phen2reg_predictor_check.rb".freeze, "bin/profile_cleaner.rb".freeze, "bin/profiles2phenopacket.rb".freeze, "bin/reg2phen.rb".freeze, "bin/region_to_patients_generator.rb".freeze, "bin/relate_CI_to_association_value.rb".freeze, "bin/setup".freeze, "example_datasets/associations_file.txt".freeze, "example_datasets/example_patient.txt".freeze, "example_datasets/example_patient_hpos.txt".freeze, "example_datasets/genes.txt".freeze, "example_datasets/hpo2ci.txt".freeze, "example_datasets/hummu_congenital_full_dataset.txt".freeze, "example_datasets/launch.sh".freeze, "external_code/generate_boxpot.R".freeze, "external_code/get_clusters.R".freeze, "external_code/install_R_dependencies.R".freeze, "external_code/lines.R".freeze, "external_code/plot_area.R".freeze, "external_code/plot_boxplot.R".freeze, "external_code/plot_density.R".freeze, "external_code/plot_heatmap.R".freeze, "external_code/plot_scatterplot.R".freeze, "external_code/plot_scatterplot_simple.R".freeze, "external_code/ronto_plotter.R".freeze, "external_code/standardize_scores.R".freeze, "external_code/xyplot_graph.R".freeze, "external_data/biosystems_gene.gz".freeze, "external_data/bsid2info.gz".freeze, "external_data/chromosome_sizes_hg18.txt".freeze, "external_data/chromosome_sizes_hg19.txt".freeze, "external_data/chromosome_sizes_hg38.txt".freeze, "external_data/gene_data.gz".freeze, "external_data/gene_data_with_pathways.gz".freeze, "external_data/gene_location.gz".freeze, "external_data/hp.json".freeze, "external_data/hp.obo".freeze, "external_data/mondo.json".freeze, "external_data/mondo.obo".freeze, "external_data/remove".freeze, "external_data/uniq_hpo_with_CI.txt".freeze, "lib/pets.rb".freeze, "lib/pets/coPatReporterMethods.rb".freeze, "lib/pets/cohort.rb".freeze, "lib/pets/common_optparse.rb".freeze, "lib/pets/constants.rb".freeze, "lib/pets/generalMethods.rb".freeze, "lib/pets/genomic_features.rb".freeze, "lib/pets/io.rb".freeze, "lib/pets/parsers/cohort_parser.rb".freeze, "lib/pets/parsers/reference_parser.rb".freeze, "lib/pets/phen2reg_methods.rb".freeze, "lib/pets/reg2phen_methods.rb".freeze, "lib/pets/version.rb".freeze, "pets.gemspec".freeze, "templates/cluster_report.erb".freeze, "templates/cohort_report.erb".freeze, "templates/evidence_profile.erb".freeze, "templates/patient_report.erb".freeze, "templates/reg2phen_report.erb".freeze, "templates/similarity_matrix.erb".freeze] s.homepage = "https://bitbucket.org/elenarojano/reg2phen/src/master/bin/reg2phen.rb".freeze s.licenses = ["MIT".freeze] s.rubygems_version = "3.5.10".freeze s.summary = "Suite with predictive tools.".freeze s.specification_version = 4 s.add_development_dependency(%q.freeze, ["~> 2.0".freeze]) s.add_development_dependency(%q.freeze, ["~> 13.0.3".freeze]) s.add_development_dependency(%q.freeze, ["~> 3.11.0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, ["~> 0.1.0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, ["~> 1.20.1".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) s.add_runtime_dependency(%q.freeze, [">= 0".freeze]) end