Files in egeulgen/pathfindR

Enrichment Analysis Utilizing Active Subnetworks

.Rbuildignore

.Rinstignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/R-CMD-check.yaml

.github/workflows/branch_naming_policy.yaml

.github/workflows/pkgdown.yaml

.github/workflows/test-coverage.yaml

.gitignore

CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

LICENSE

LICENSE.md

NAMESPACE

NEWS.md R/active_snw_search.R R/clustering.R R/comparison.R R/core.R R/data_generation.R R/enrichment.R R/pathfindr.R R/scoring.R R/utility.R R/visualization.R R/zzz.R README.Rmd README.md

_pkgdown.yml

codecov.yml

cran-comments.md

inst/CITATION

inst/extdata/CREB.txt

inst/extdata/MYC.txt

inst/extdata/logo.png

inst/extdata/resultActiveSubnetworkSearch.txt

inst/java/ActiveSubnetworkSearch.jar

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

java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java

java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java

java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java

java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java

java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java

java/ActiveSubnetworkSearchMisc/Gaussian.java

java/ActiveSubnetworkSearchMisc/ScoreCalculations.java

java/ActiveSubnetworkSearchMisc/Subnetwork.java

java/ActiveSubnetworkSearchMisc/ZStatistics.java

java/Application/AppActiveSubnetworkSearch.java

java/Application/Parameters.java

java/File/ExperimentFileReader.java

java/File/SIFReader.java

java/Network/Network.java

java/Network/Node.java

java/Network/SubnetworkFinder.java

man/UpSet_plot.Rd man/active_snw_enrichment_wrapper.Rd man/active_snw_search.Rd man/annotate_term_genes.Rd man/check_java_version.Rd man/cluster_enriched_terms.Rd man/cluster_graph_vis.Rd man/color_kegg_pathway.Rd man/combine_pathfindR_results.Rd man/combined_results_graph.Rd man/configure_output_dir.Rd man/create_HTML_report.Rd man/create_kappa_matrix.Rd man/enrichment.Rd man/enrichment_analyses.Rd man/enrichment_chart.Rd man/fetch_gene_set.Rd man/fetch_java_version.Rd

man/figures/apple-touch-icon-120x120.png

man/figures/apple-touch-icon-152x152.png

man/figures/apple-touch-icon-180x180.png

man/figures/apple-touch-icon-60x60.png

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man/figures/apple-touch-icon.png

man/figures/favicon-16x16.png

man/figures/favicon-32x32.png

man/figures/favicon.ico

man/filterActiveSnws.Rd man/fuzzy_term_clustering.Rd man/get_biogrid_pin.Rd man/get_gene_sets_list.Rd man/get_kegg_gsets.Rd man/get_mgsigdb_gsets.Rd man/get_pin_file.Rd man/get_reactome_gsets.Rd man/gset_list_from_gmt.Rd man/hierarchical_term_clustering.Rd man/hyperg_test.Rd man/input_processing.Rd man/input_testing.Rd man/isColor.Rd man/pathfindr.Rd man/plot_scores.Rd man/process_pin.Rd man/return_pin_path.Rd man/run_pathfindr.Rd man/score_terms.Rd man/single_iter_wrapper.Rd man/summarize_enrichment_results.Rd man/term_gene_graph.Rd man/term_gene_heatmap.Rd man/visualize_KEGG_diagram.Rd man/visualize_active_subnetworks.Rd man/visualize_term_interactions.Rd man/visualize_terms.Rd

revdep/.gitignore

revdep/email.yml

revdep/failures.md slides/cost_charme_school/cost_charme_school.pdf slides/cost_charme_school/demo_script.R slides/episystem_workshop.pdf slides/v1.4_presentation/pathfindR_v1.4.pdf slides/v1.5_presentation/pathfindR_v1.5.pdf slides/v2.4_presentation/pathfindR_v2.4.pdf slides/v2_presentation/pathfindR_v2.pdf tests/testthat-active_snw.R tests/testthat-clustering.R tests/testthat-comparison.R tests/testthat-core.R tests/testthat-data_generation.R tests/testthat-enrichment.R tests/testthat-scoring.R tests/testthat-utility.R tests/testthat-visualization.R tests/testthat-zzz.R tests/testthat/test-active_snw_search.R tests/testthat/test-clustering.R tests/testthat/test-comparison.R tests/testthat/test-core.R tests/testthat/test-data_generation.R tests/testthat/test-enrichment.R tests/testthat/test-scoring.R tests/testthat/test-utility.R tests/testthat/test-visualization.R tests/testthat/test-zzz.R

vignettes/.gitignore

vignettes/combined_graph.png

vignettes/comparing_results.Rmd

vignettes/enrichment_chart.png

vignettes/example_interaction_vis.png

vignettes/example_kegg_pathway_diagram.png

vignettes/hmap.png

vignettes/intro_vignette.Rmd

vignettes/man_enrichment_chart.png

vignettes/manual_execution.Rmd vignettes/non_hs_analysis.Rmd vignettes/obtain_data.Rmd

vignettes/pathfindr.png

vignettes/score_hmap.png

vignettes/term_clustering.png

vignettes/term_gene.png

vignettes/upset.png

vignettes/visualization_vignette.Rmd

egeulgen/pathfindR documentation built on May 3, 2024, 3:15 a.m.