Files in pathfindR
Enrichment Analysis Utilizing Active Subnetworks
.Rinstignore
MD5
NEWS.md
NAMESPACE
DESCRIPTION
LICENSE
java/Application/AppActiveSubnetworkSearch.java
java/Application/Parameters.java
java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
java/File/SIFReader.java
java/File/ExperimentFileReader.java
java/Network/Node.java
java/Network/SubnetworkFinder.java
java/Network/Network.java
java/ActiveSubnetworkSearchMisc/Subnetwork.java
java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
java/ActiveSubnetworkSearchMisc/ZStatistics.java
java/ActiveSubnetworkSearchMisc/Gaussian.java
R/core.R
R/visualization.R
R/enrichment.R
R/data_generation.R
R/comparison.R
R/clustering.R
R/active_snw_search.R
R/utility.R
R/zzz.R
R/pathfindr.R
R/scoring.R
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/manual_execution.R
inst/doc/obtain_data.html
inst/doc/manual_execution.Rmd
inst/doc/manual_execution.html
inst/doc/comparing_results.Rmd
inst/doc/obtain_data.R
inst/doc/visualization_vignette.Rmd
inst/java/ActiveSubnetworkSearch.jar
inst/extdata/resultActiveSubnetworkSearch.txt
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-active_snw.R
tests/testthat-zzz.R
tests/testthat-data_generation.R
tests/testthat-clustering.R
tests/testthat-utility.R
tests/testthat-scoring.R
tests/testthat-visualization.R
tests/testthat-enrichment.R
tests/testthat-comparison.R
tests/testthat-core.R
tests/testthat/test-zzz.R
tests/testthat/test-data_generation.R
tests/testthat/test-active_snw_search.R
tests/testthat/test-clustering.R
tests/testthat/test-enrichment.R
tests/testthat/test-utility.R
tests/testthat/test-scoring.R
tests/testthat/test-comparison.R
tests/testthat/test-core.R
tests/testthat/test-visualization.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/manual_execution.Rmd
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
man/enrichment_chart.Rd
man/score_terms.Rd
man/term_gene_graph.Rd
man/single_iter_wrapper.Rd
man/combine_pathfindR_results.Rd
man/fetch_gene_set.Rd
man/pathfindR.Rd
man/visualize_KEGG_diagram.Rd
man/configure_output_dir.Rd
man/check_java_version.Rd
man/run_pathfindR.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/combined_results_graph.Rd
man/get_reactome_gsets.Rd
man/term_gene_heatmap.Rd
man/get_kegg_gsets.Rd
man/filterActiveSnws.Rd
man/visualize_terms.Rd
man/cluster_graph_vis.Rd
man/visualize_term_interactions.Rd
man/annotate_term_genes.Rd
man/create_HTML_report.Rd
man/hyperg_test.Rd
man/UpSet_plot.Rd
man/cluster_enriched_terms.Rd
man/input_processing.Rd
man/active_snw_enrichment_wrapper.Rd
man/enrichment.Rd
man/plot_scores.Rd
man/create_kappa_matrix.Rd
man/enrichment_analyses.Rd
man/color_kegg_pathway.Rd
man/isColor.Rd
man/visualize_active_subnetworks.Rd
man/get_biogrid_pin.Rd
man/fuzzy_term_clustering.Rd
man/fetch_java_version.Rd
man/get_mgsigdb_gsets.Rd
man/active_snw_search.Rd
man/get_pin_file.Rd
man/hierarchical_term_clustering.Rd
man/get_gene_sets_list.Rd
man/figures/apple-touch-icon-76x76.png
man/figures/apple-touch-icon-120x120.png
man/figures/favicon-16x16.png
man/figures/apple-touch-icon-180x180.png
man/figures/favicon.ico
man/figures/favicon-32x32.png
man/figures/apple-touch-icon.png
man/figures/apple-touch-icon-152x152.png
man/figures/apple-touch-icon-60x60.png
