Files in pathfindR

Enrichment Analysis Utilizing Active Subnetworks

.Rinstignore

MD5

NEWS.md

NAMESPACE

DESCRIPTION

LICENSE

R/RcppExports.R R/util_input_testing_processing.R R/active_snw_filtering.R R/active_snw_search_greedy.R R/visualize_term_gene_graph.R R/pathfindR-package.R R/data.R R/enrichment.R R/data_generation.R R/comparison.R R/active_snw_search_sa.R R/clustering.R R/active_snw_search_and_enrichment_wrapper.R R/util-visualization.R R/util_fetch_gene_sets.R R/util_interaction_files.R R/visualize_term_gene_heatmap.R R/active_snw_search_score.R R/visualize_enrichment_chart.R R/active_snw_identification_pipeline.R R/active_snw_search_ga.R R/active_snw_search_main.R R/util_output_processing.R R/visualize_clustering_graph.R R/visualize_upset_plot.R R/visualize_active_snw.R R/visualize_terms.R R/scoring.R R/run_pathfindr.R R/active_snw_search_utils.R

src/java_compat.h

src/RcppExports.cpp

src/subnetwork_scoring.cpp

src/pathfindR-package.cpp

src/greedy_search.cpp

src/simulated_annealing.cpp

src/score_calculation_utils.cpp

src/java_compat.cpp

inst/CITATION

inst/doc/non_hs_analysis.html

inst/doc/non_hs_analysis.Rmd

inst/doc/intro_vignette.html

inst/doc/comparing_results.R inst/doc/intro_vignette.Rmd inst/doc/intro_vignette.R

inst/doc/visualization_vignette.html

inst/doc/obtain_data.Rmd inst/doc/visualization_vignette.R

inst/doc/comparing_results.html

inst/doc/non_hs_analysis.R

inst/doc/obtain_data.html

inst/doc/comparing_results.Rmd inst/doc/obtain_data.R inst/doc/visualization_vignette.Rmd

inst/extdata/logo.png

inst/extdata/CREB.txt

inst/extdata/MYC.txt

inst/rmd/enriched_terms.Rmd inst/rmd/results.Rmd inst/rmd/conversion_table.Rmd

build/vignette.rds

tests/testthat-data_generation.R tests/testthat-clustering.R tests/testthat-cpp.R tests/testthat-utility.R tests/testthat-run-pathfindr.R tests/testthat-search-and-enrichment-wrapper.R tests/testthat-scoring.R tests/testthat-active-snw.R tests/testthat-visualization.R tests/testthat-enrichment.R tests/testthat-comparison.R tests/testthat/test-visualize-terms.R tests/testthat/test-search-and-enrichment-wrapper.R tests/testthat/test-active-snw-identification-pipeline.R tests/testthat/test-cpp-score-calculation-utils.R tests/testthat/test-visualize-clustering-graph.R tests/testthat/test-data_generation.R tests/testthat/test-active-snw-search-sa.R tests/testthat/test-visualize-upset-plot.R tests/testthat/test-cpp-greedy-search.R tests/testthat/test-util-output-processing.R tests/testthat/test-visualize-term-gene-graph.R tests/testthat/test-clustering.R tests/testthat/test-active-snw-seach-score.R tests/testthat/test-util-fetch-gene-sets.R tests/testthat/test-util-input-testing-processing.R tests/testthat/test-visualize-term-gene-heatmap.R tests/testthat/test-util-visualization.R tests/testthat/test-run-pathfindr.R tests/testthat/test-enrichment.R tests/testthat/test-active-snw-search-ga.R tests/testthat/test-visualize-active-subnetworks.R tests/testthat/test-util-interaction-files.R tests/testthat/test-scoring.R tests/testthat/test-comparison.R tests/testthat/test-visualize-enrichment-chart.R tests/testthat/test-active-snw-search-main.R tests/testthat/test-active-snw-search-utils.R tests/testthat/test-active-snw-filtering.R tests/testthat/test-active-snw-search-greedy.R

vignettes/enrichment_chart.png

vignettes/term_clustering.png

vignettes/non_hs_analysis.Rmd

vignettes/combined_graph.png

vignettes/intro_vignette.Rmd

vignettes/example_kegg_pathway_diagram.png

vignettes/obtain_data.Rmd

vignettes/example_interaction_vis.png

vignettes/hmap.png

vignettes/man_enrichment_chart.png

vignettes/pathfindr.png

vignettes/upset.png

vignettes/comparing_results.Rmd

vignettes/term_gene.png

vignettes/score_hmap.png

vignettes/visualization_vignette.Rmd

data/example_unfiltered_snws.rda

man/enrichment_chart.Rd man/score_terms.Rd man/dot-ga_make_individual.Rd man/create_term_gene_graph.Rd man/single_iter_wrapper.Rd man/combine_pathfindR_results.Rd man/create_term_gene_plot.Rd man/pathfindR.Rd man/visualize_KEGG_diagram.Rd man/run_pathfindR.Rd man/build_network.Rd man/dot-ga_compare.Rd man/return_pin_path.Rd man/input_testing.Rd man/gset_list_from_gmt.Rd man/process_pin.Rd man/summarize_enrichment_results.Rd man/dot-ga_score.Rd man/dot-ga_sort_desc.Rd man/combined_results_graph.Rd man/dot-make_subnetwork.Rd man/get_reactome_gsets.Rd man/dot-find_subnetworks.Rd man/term_gene_heatmap.Rd man/get_kegg_gsets.Rd man/dot-ga_pick.Rd man/visualize_terms.Rd man/cluster_graph_vis.Rd man/dot-greedy_search.Rd man/visualize_term_interactions.Rd man/annotate_term_genes.Rd man/build_score_context.Rd man/get_active_subnetworks.Rd man/create_HTML_report.Rd man/dot-genetic_algorithm.Rd man/hyperg_test.Rd man/fetch_gene_sets.Rd man/UpSet_plot.Rd man/cluster_enriched_terms.Rd man/input_processing.Rd man/safe_get_content.Rd man/active_subnetwork_search.Rd man/active_snw_enrichment_wrapper.Rd man/enrichment.Rd man/plot_scores.Rd man/filter_active_subnetworks.Rd man/create_kappa_matrix.Rd man/enrichment_analyses.Rd man/dot-parse_experiment.Rd man/dot-ga_crossover_mutation.Rd man/color_kegg_pathway.Rd man/isColor.Rd man/example_unfiltered_snws.Rd man/dot-sort_subnetworks_desc.Rd man/visualize_active_subnetworks.Rd man/get_biogrid_pin.Rd man/order_df_by_columnn.Rd man/fuzzy_term_clustering.Rd man/get_mgsigdb_gsets.Rd man/dot-find_components_named.Rd man/get_pin_file.Rd man/hierarchical_term_clustering.Rd man/dot-simulated_annealing.Rd man/dot-score_subnetwork.Rd man/get_gene_sets_list.Rd

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pathfindR documentation built on July 2, 2026, 1:06 a.m.