Files in egeulgen/pathfindR
Pathway Enrichment Analysis Utilizing Active Subnetworks

.Rbuildignore
.Rinstignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/active_snw_functions.R R/clustering.R R/core_functions.R R/data.R R/enrichment_functions.R R/pathfindr.R R/scores.R R/visualization_functions.R README.md cran-comments.md
data/RA_clustered.rda
data/RA_exp_mat.rda
data/RA_input.rda
data/RA_output.rda
data/biocarta_genes.rda
data/biocarta_pathways.rda
data/custom_result.rda
data/example_active_snws.rda
data/go_all_genes.rda
data/go_all_pathways.rda
data/go_bp_genes.rda
data/go_bp_pathways.rda
data/go_cc_genes.rda
data/go_cc_pathways.rda
data/go_mf_genes.rda
data/go_mf_pathways.rda
data/kegg_genes.rda
data/kegg_pathways.rda
data/reactome_genes.rda
data/reactome_pathways.rda
inst/CITATION
inst/extdata/Biogrid.sif
inst/extdata/CREB.txt
inst/extdata/GeneMania.sif
inst/extdata/IntAct.sif
inst/extdata/KEGG.sif
inst/extdata/MYC.txt
inst/extdata/resultActiveSubnetworkSearch.txt
inst/java/ActiveSubnetworkSearch.jar
inst/rmd/conversion_table.Rmd inst/rmd/enriched_pathways.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/RA_clustered.Rd man/RA_exp_mat.Rd man/RA_input.Rd man/RA_output.Rd man/active_snw_search.Rd man/annotate_pathway_DEGs.Rd man/biocarta_genes.Rd man/biocarta_pathways.Rd man/calculate_pw_scores.Rd man/cluster_graph_vis.Rd man/cluster_pathways.Rd man/create_kappa_matrix.Rd man/custom_result.Rd man/enrichment.Rd man/enrichment_analyses.Rd man/enrichment_chart.Rd man/example_active_snws.Rd man/filterActiveSnws.Rd man/fuzzy_pw_clustering.Rd man/go_all_genes.Rd man/go_all_pathways.Rd man/go_bp_genes.Rd man/go_bp_pathways.Rd man/go_cc_genes.Rd man/go_cc_pathways.Rd man/go_mf_genes.Rd man/go_mf_pathways.Rd man/hierarchical_pw_clustering.Rd man/hyperg_test.Rd man/input_processing.Rd man/input_testing.Rd man/kegg_genes.Rd man/kegg_pathways.Rd man/pathfindr.Rd man/plot_scores.Rd man/reactome_genes.Rd man/reactome_pathways.Rd man/return_pin_path.Rd man/run_pathfindr.Rd man/summarize_enrichment_results.Rd man/visualize_hsa_KEGG.Rd man/visualize_pw_interactions.Rd man/visualize_pws.Rd
vignettes/.gitignore
vignettes/example_pw_vis.png
vignettes/pathfindr.png
vignettes/pathfindr_manual_exec.Rmd vignettes/pathfindr_vignette.Rmd
vignettes/pw_clustering.png
vignettes/pw_score_hmap.png
egeulgen/pathfindR documentation built on Nov. 28, 2018, 3:07 p.m.