553b1b26a878d2414c7377ea0c07ad8b *DESCRIPTION
ea744e0e8897a52f830dda39e0f51791 *LICENSE
f67f356dd2068620d5e91ac22a5b70fe *NAMESPACE
9f8ef6337af6af76be6c57e53e6bfbd1 *NEWS.md
b96a2535ede5a7546082394fc8022790 *R/active_snw_search.R
d2b2c9032c0d95fad14af0fb709ade70 *R/clustering.R
bdb4b7544526838181e8b0d803dce677 *R/comparison.R
2f6736f730fd1282dfa2b5df88e8ec16 *R/core.R
f63bc76e2afa02e0ff2cf8f865a1ce59 *R/data_generation.R
21f561f83013df8dae6ee811995cb2e4 *R/enrichment.R
eec6dd4145373f80caf37bf4d05c9eb4 *R/pathfindr.R
15969d86a3f8b3b936bb5236c9b71fbd *R/scoring.R
efc6aae5e70cb5b439f7fa75e7e0bb5b *R/utility.R
be2be8cde11cc43eea875947740800ae *R/visualization.R
47fdb88b2d71a97847bbb1e0d5ef57df *R/zzz.R
f3fd18fa02a7bae4e31d057f5c32d18c *build/vignette.rds
9e1af9184114ac649e898bdaa1262a95 *inst/CITATION
f37908b821502bbce032be42db0edecf *inst/doc/comparing_results.R
435fd14fe05ec8bc0a958db923210ec5 *inst/doc/comparing_results.Rmd
d93bb274228bc0566028716baf498b1a *inst/doc/comparing_results.html
3cc9d885dcf426704592dd89ce1fd5f6 *inst/doc/intro_vignette.R
cef2d9c458716c9351adcc86001b67d2 *inst/doc/intro_vignette.Rmd
c0f2bb0ba7880053ed698c16cc18e39f *inst/doc/intro_vignette.html
0c12858c02b4c09f1ce5395702f7c98b *inst/doc/manual_execution.R
ff18be28f2bd57806e9371cbdbfb85dc *inst/doc/manual_execution.Rmd
578bdc96d64a3a80b359c5e9aa361898 *inst/doc/manual_execution.html
a6d47786e7b1efdfc8b2312072c56123 *inst/doc/non_hs_analysis.R
606eaf2e246d4d032a312f6b669cc3ee *inst/doc/non_hs_analysis.Rmd
9b6a8dc40e4c340abd7915296105d383 *inst/doc/non_hs_analysis.html
24a7d2e64e246fee2885b0aa4d91a815 *inst/doc/obtain_data.R
5ec28e6dc87eafd90cd341a84edace55 *inst/doc/obtain_data.Rmd
a0caa603bd2e13d4c388232efbe24cbf *inst/doc/obtain_data.html
6370540ebe25111124387ae10be0863d *inst/doc/visualization_vignette.R
5f89aad61bc9987be17fd686aacb6fe0 *inst/doc/visualization_vignette.Rmd
6b9ba1deca9d95b2a3123ea426c49d48 *inst/doc/visualization_vignette.html
45ee26db5b65613aceacb9e64733ee2f *inst/extdata/CREB.txt
aa1874ac25cbf1fcccbf8c3e3d9d6a9a *inst/extdata/MYC.txt
329f3582fd545de9b88e50b38da79650 *inst/extdata/logo.png
93fcf75a09daf8545279fa9fb79f0284 *inst/extdata/resultActiveSubnetworkSearch.txt
c7f1196d0d4bdb56fe598cf7d9ac670a *inst/java/ActiveSubnetworkSearch.jar
17b225d9bc6c49890c4268eb12a882e1 *inst/rmd/conversion_table.Rmd
4dbb0ff7e516460af0706582a704755e *inst/rmd/enriched_terms.Rmd
4165bca20af768a694cd12a0b59b29b4 *inst/rmd/results.Rmd
5aefed1e6692c2d69686853966feb72d *java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
9732f3a20f8bfe3aae4a3182175cf9be *java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
d6fcb522b12e6bde21f83424ed55d164 *java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
c489bd5c01cf42e159e1ee3809ac3700 *java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
ece8ea7d6380af5b51d69bcf25ab6b1a *java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
f0aae5d87de27c5883efa7f10a4f0764 *java/ActiveSubnetworkSearchMisc/Gaussian.java
f36f34e964503625947828d4c227019e *java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
b8cea43205699d2ced1cdac423e32baa *java/ActiveSubnetworkSearchMisc/Subnetwork.java
5577bdbec43ecfb930293c24a5c3ef2e *java/ActiveSubnetworkSearchMisc/ZStatistics.java
c724a1c1bcd5c07546c79515bf70c9e8 *java/Application/AppActiveSubnetworkSearch.java
d38e1e57acb81826eabbb508e8b36734 *java/Application/Parameters.java
0fa2a07024c2853b88a08997ad81463a *java/File/ExperimentFileReader.java
b4fbea34bdf79841a729be5055f31307 *java/File/SIFReader.java
1a5b64f7fa93e6e2d6e5c7d1c4a67582 *java/Network/Network.java
f516e3c30a9953abaf0f48ab54de9a9e *java/Network/Node.java
fb9a95c51d77dbb3580f57c63c9582ea *java/Network/SubnetworkFinder.java
6c5c10a0601f8e3dfb6d04d97c624c1e *man/UpSet_plot.Rd
3b80193f6cdc818e26482c5a84265a26 *man/active_snw_enrichment_wrapper.Rd
5e5933dd928e9247359b17626e16ba47 *man/active_snw_search.Rd
3fc6fb0a61430c84fa55f66a0878edfc *man/annotate_term_genes.Rd
cf4b6a38eb235e277da5974c5b3f34f0 *man/check_java_version.Rd
a689d6a2dcd26bacb783ed059cae926c *man/cluster_enriched_terms.Rd
becf804f0413216947b1d8678ee53be4 *man/cluster_graph_vis.Rd
4d36d8b3e1a1e092998b611cf508d2e3 *man/color_kegg_pathway.Rd
94cb862e515b8d2ee01acf0c012e73b0 *man/combine_pathfindR_results.Rd
94f4f4cfe351a8ab2029204f2e2488cb *man/combined_results_graph.Rd
513c3a7bead6f80aca1b00a66d407aef *man/configure_output_dir.Rd
3de51e285070a20a51da3323adfadb6b *man/create_HTML_report.Rd
796926bffd51cdd2b17aa2d1d81d8df6 *man/create_kappa_matrix.Rd
34b415ffb517f9f7e234fe61ebb7471b *man/download_kegg_png.Rd
c266f999be7a8010c23cdd17887651e2 *man/enrichment.Rd
cbd3eae15f4ba495aea40185088bb3e4 *man/enrichment_analyses.Rd
7b00a9064bf8df6d4ce5392ed087ca6c *man/enrichment_chart.Rd
891244df3d8aa210f6df0f90337ff1d5 *man/fetch_gene_set.Rd
3aa669268562c410d89e6e31fd8c1e7c *man/fetch_java_version.Rd
ecc2814289181b838e77711f6d711255 *man/figures/apple-touch-icon-120x120.png
c25da64e08495e0fb2063f91ad8edfc5 *man/figures/apple-touch-icon-152x152.png
32f41210fe875bbea846f26d4bf1c73f *man/figures/apple-touch-icon-180x180.png
18b2fde00028fef101634d4c0aa0d9ab *man/figures/apple-touch-icon-60x60.png
d19cbd2384dc75b1c0e126c3c8ce32e7 *man/figures/apple-touch-icon-76x76.png
32f41210fe875bbea846f26d4bf1c73f *man/figures/apple-touch-icon.png
4063155e4115ab35c5f110493690a285 *man/figures/favicon-16x16.png
c6586c87c68e00f6b9b31a43baba779f *man/figures/favicon-32x32.png
4bf0edf00f09745738b778f969b79745 *man/figures/favicon.ico
c06c0340d8edd79cee525f13da59ee31 *man/filterActiveSnws.Rd
41ac2c3eed67ef0a46e5e7cc08054b7a *man/fuzzy_term_clustering.Rd
0597003aacbe8521340c1a271bf59b8e *man/get_biogrid_pin.Rd
ffa39f4e074085e1b1d8822e629468f6 *man/get_gene_sets_list.Rd
077aa9d07ce441f6c0693fffdd5188fc *man/get_kegg_gsets.Rd
8ae641e598ea1b70a33230d9785f8a0e *man/get_mgsigdb_gsets.Rd
370d404b8bf5e9251684e1c0238b7bad *man/get_pin_file.Rd
5caca1c0244aeae65f5c64dd2462be20 *man/get_reactome_gsets.Rd
864ff3d76d9a7af4608e49112299ee80 *man/gset_list_from_gmt.Rd
12546adaeece4a2291dbfba563b2e02b *man/hierarchical_term_clustering.Rd
91689f3100ea21865b1433ba128ffd9f *man/hyperg_test.Rd
51e3faf0dae98db0ad39bfcc3959d355 *man/input_processing.Rd
83bee5929ffcd00303dc9de35aade60e *man/input_testing.Rd
fd8f9d18daae37b3f03a94a53456bdb1 *man/obtain_KEGGML_URL.Rd
d24c9cc1d49db0591c63142bfe355515 *man/obtain_colored_url.Rd
eeb40099adee8a0e221961145a30ee61 *man/pathfindR.Rd
c2ceaac3a8dc8d4f92e3214f4d71f2f1 *man/plot_scores.Rd
377d84c8f66bb22644b0c271fc8492bb *man/process_pin.Rd
3b66c9d17bd399e5f1c105f6bb40d7fb *man/return_pin_path.Rd
552101bca7e7502fdd0a84b84da4988f *man/run_pathfindR.Rd
d11b9ed59cee5854bee99ca228a4b666 *man/score_terms.Rd
d53430e07a5e9a1a3c8af3e5c9f7d2b8 *man/summarize_enrichment_results.Rd
dd4cf5e2d6a2d6c1b6fd82b36288abd5 *man/term_gene_graph.Rd
e91903b903c695f703fbc23a0e195c45 *man/term_gene_heatmap.Rd
2096eb7f55b4a08b06192dd7bcc746e0 *man/visualize_active_subnetworks.Rd
449395c3808a8ecc4912178aa065aa4f *man/visualize_hsa_KEGG.Rd
83b908cdedfc4674f2dc46507912125e *man/visualize_term_interactions.Rd
b2c9d9dada1b23de331e64c3eebb5024 *man/visualize_terms.Rd
5896b8500bc1ed44820de04fc3ac8223 *tests/testthat-active_snw.R
21c6c5d7b199e29921c376178863d1b1 *tests/testthat-clustering.R
d9829ccb93600a3707800adb8b634fe0 *tests/testthat-comparison.R
3028f47958c7bfdebf4a71b7f0aa227c *tests/testthat-core.R
5e35dabaafc90adf64bd24a042e3c348 *tests/testthat-data_generation.R
828eafccc03e9b2a535b760f28462f0a *tests/testthat-enrichment.R
657d7b43c441f40c8db562dfff5670a8 *tests/testthat-scoring.R
703271eac97fa3b2d71fc69ce091fbb4 *tests/testthat-utility.R
cea41be85dac3d55c4709f1437d63d31 *tests/testthat-visualization.R
cd28da8ea9a1e0450b217661f653c00f *tests/testthat-zzz.R
5f9b744883f466ab38b1620fc73bf484 *tests/testthat/test-active_snw_search.R
a24b7b0405ad0da0a675b32e226d475a *tests/testthat/test-clustering.R
ee9337d6921823ef461e597ec4f31670 *tests/testthat/test-comparison.R
c1a0e30d84079df548e0f433c8ad9037 *tests/testthat/test-core.R
99890790aa79fe790404e1603cbbb946 *tests/testthat/test-data_generation.R
4c6b2269edf4d14325fa7f19eb81a832 *tests/testthat/test-enrichment.R
286c9e287be450dc0571294a8de2d9dc *tests/testthat/test-scoring.R
833674f22021d2b1d0bc37cd778af3c1 *tests/testthat/test-utility.R
05d1d38f65adceca61c74c4f3cb8554c *tests/testthat/test-visualization.R
3ab5d3d5b358afabeda984450a9818ae *tests/testthat/test-zzz.R
bdac24c9d00f660cb99fc25c500292b7 *vignettes/combined_graph.png
435fd14fe05ec8bc0a958db923210ec5 *vignettes/comparing_results.Rmd
415837792f36547fbc292f729b816245 *vignettes/enrichment_chart.png
e0ded256aeea286bb001a9a89ca56fb5 *vignettes/example_interaction_vis.png
039786da126d2faac382071193851869 *vignettes/hmap.png
330b072c7aa40a4d8e52f0674cfd4638 *vignettes/hsaKEGG_diagram.png
cef2d9c458716c9351adcc86001b67d2 *vignettes/intro_vignette.Rmd
157c5aa448fee542c18ad3314013b450 *vignettes/man_enrichment_chart.png
ff18be28f2bd57806e9371cbdbfb85dc *vignettes/manual_execution.Rmd
606eaf2e246d4d032a312f6b669cc3ee *vignettes/non_hs_analysis.Rmd
5ec28e6dc87eafd90cd341a84edace55 *vignettes/obtain_data.Rmd
2e99533464a30126c1382db953397487 *vignettes/pathfindr.png
de8bae33cf62e8766ba986fbab02427e *vignettes/score_hmap.png
2b28501360bad9a8edd42daa83756854 *vignettes/term_clustering.png
4611e3e03e736f4193b8e431ae49144c *vignettes/term_gene.png
92aa705c12da29ad00b5daec100a8ac5 *vignettes/upset.png
5f89aad61bc9987be17fd686aacb6fe0 *vignettes/visualization_vignette.Rmd
