Files in neurogenomics/HPOExplorer

Analysis and Visualisation of the Human Phenotype Ontology

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md NEWS.md R/0docs.R R/add_ancestor.R R/add_death.R R/add_disease.R R/add_disease_genes.R R/add_evidence.R R/add_gene_frequency.R R/add_genes.R R/add_gpt_annotations.R R/add_hpo_definition.R R/add_hpo_id.R R/add_hpo_name.R R/add_hpo_synonym.R R/add_info_content.R R/add_mondo.R R/add_ndisease.R R/add_omop.R R/add_onset.R R/add_ont_lvl.R R/add_pheno_frequency.R R/add_prevalence.R R/add_prevalence_report.R R/add_severity.R R/add_tier.R R/annotate_phenos.R R/as_ascii.R R/data.R R/example_phenos.R R/filter_descendants.R R/fix_hpo_ids.R R/get_data.R R/get_freq_dict.R R/get_gene_lists.R R/get_hpo.R R/get_hpo_id_direct.R R/get_mappings.R R/get_term_definition_api.R R/get_term_definition_data.R R/get_top_phenos.R R/gpt_annot_check.R R/gpt_annot_check_plot.R R/gpt_annot_class.R R/gpt_annot_codify.R R/gpt_annot_melt.R R/gpt_annot_plot.R R/gpt_annot_plot_branches.R R/gpt_annot_read.R R/hpo_api.R R/hpo_death_agg.R R/hpo_dict.R R/hpo_frequencies_agg.R R/hpo_modifiers_agg.R R/hpo_onsets_agg.R R/hpo_to_matrix.R R/list_columns.R R/list_deaths.R R/list_onsets.R R/load_phenotype_to_genes.R R/make_igraph_object.R R/make_network_object.R R/make_network_plot.R R/make_node_data.R R/make_phenos_dataframe.R R/make_tiers.R R/map_disease.R R/map_phenotypes.R R/message_parallel.R R/messager.R R/newlines_to_definition.R R/parse_frequency.R R/parse_pheno_frequency.R R/per_branch_plot.R R/phenos_to_granges.R R/pkg_data.R R/plot_arrow.R R/plot_evidence.R R/plot_top_phenos.R R/report_missing.R R/search_hpo.R R/unlist_col.R README.Rmd README.md inst/hex/hexSticker.Rmd man/add_.Rd man/add_disease.Rd man/disease_id_to_omop.Rd man/disease_map.Rd man/filter_.Rd man/fix_hpo_ids.Rd man/get_.Rd man/get_data.Rd man/get_gene_lists.Rd man/get_term_definition_api.Rd man/get_top_phenos.Rd man/gpt_annot_check.Rd man/gpt_annot_class.Rd man/gpt_annot_codify.Rd man/gpt_annot_melt.Rd man/gpt_annot_plot.Rd man/gpt_annot_plot_branches.Rd man/gpt_annot_read.Rd man/hpo_api.Rd man/hpo_deaths.Rd man/hpo_frequencies.Rd man/hpo_id_to_omop.Rd man/hpo_modifiers.Rd man/hpo_onsets.Rd man/hpo_tiers.Rd man/hpo_tiers_auto.Rd man/hpo_to_matrix.Rd man/list_columns.Rd man/load_phenotype_to_genes.Rd man/main.Rd man/make_.Rd man/map_.Rd man/map_disease.Rd man/map_phenotypes.Rd man/newlines_to_definition.Rd man/per_branch_plot.Rd man/phenos_to_granges.Rd man/plot_arrow.Rd man/plot_evidence.Rd man/plot_top_phenos.Rd man/search_hpo.Rd man/unlist_col.Rd tests/testthat.R tests/testthat/Rplots.pdf tests/testthat/test-add_disease.R tests/testthat/test-add_evidence.R tests/testthat/test-add_gene_frequency.R tests/testthat/test-add_hpo_id.R tests/testthat/test-add_info_content.R tests/testthat/test-add_omop.R tests/testthat/test-add_ont_lvl.R tests/testthat/test-add_pheno_frequency.R tests/testthat/test-add_tier.R tests/testthat/test-as_ascii.R tests/testthat/test-filter_descendants.R tests/testthat/test-get_gene_lists.R tests/testthat/test-get_hpo.R tests/testthat/test-gpt_annot_check.R tests/testthat/test-gpt_annot_codify.R tests/testthat/test-gpt_annot_plot_branches.R tests/testthat/test-hpo_to_matrix.R tests/testthat/test-list_onsets.R tests/testthat/test-load_phenotype_to_genes.R tests/testthat/test-make_network_plot.R tests/testthat/test-make_phenos_dataframe.R tests/testthat/test-make_tiers.R tests/testthat/test-per_branch_plot.R tests/testthat/test-phenos_to_granges.R tests/testthat/test-plot_graph_3d.R vignettes/HPOExplorer.Rmd vignettes/docker.Rmd