77b4108ef465cf31b488df66b32a7a0c *DESCRIPTION
647a602266f7455f9d09b0ce48206a1b *LICENSE
cf00ffc78830615884a701a7ea3b84e7 *NAMESPACE
943f0dd75a63d20fe4210b282861c22d *NEWS.md
abfca385ccbaa647d40eb3bfba0d5c5a *R/active_snw_functions.R
3729b6ea08636367848c36b3af7dd077 *R/clustering_functions.R
11c8c1c34450bad789542777ef5a7cf7 *R/core_functions.R
05bfbb361ea5947f5244ee4cc4d7596b *R/data.R
14434966f8aa614a862b49edc861a50b *R/enrichment_functions.R
12f9939b984fccd60fcb4ea80d728115 *R/pathfindR.R
7db0bc07e11cd22e23e97c68ea5e500d *R/scoring.R
35644deff401edb98407aaeafdf131d1 *R/sysdata.rda
0f855a3bdc61f2ef0faff17534a9818a *R/visualization_functions.R
7ab9b339906c95c6f34feaa9ddb1b7cc *build/vignette.rds
d49790dcdf5b59f4d5ff0d0e45edf3f1 *data/RA_clustered.rda
802cfde2f633f4b83e4d420ae89eb6cb *data/RA_exp_mat.rda
f9b6f0bf7cb62a55d8dca0b3195e3f75 *data/RA_input.rda
a4aa13ceebbdce5c5b314330c4f71cca *data/RA_output.rda
d5f5038d1eadfeb63261da7474ab0b2a *data/biocarta_descriptions.rda
ca3aba76e6a90b374aa03b6ab8b84520 *data/biocarta_genes.rda
151fca799787c3e3b21c72b0f365b61e *data/custom_result.rda
48380d228cbe53fcd49e6d3b5f9d365d *data/example_active_snws.rda
445178e33dde83ee97dc8e90a769b194 *data/go_all_genes.rda
686d6fba171f5bdb04173e51ea06a9e1 *data/kegg_descriptions.rda
8d9e555e78b36e170ba18156c240527a *data/kegg_genes.rda
55e23ad8b5c80aba4856899abcd7226d *data/mmu_kegg_descriptions.rda
e6e4ac7ec9097b0a5c823ccbebc6460f *data/mmu_kegg_genes.rda
84390e7c2bc6257b324af54104d562b4 *data/myeloma_input.rda
31d1961139f2aba1adc1a018f9c1b5b3 *data/myeloma_output.rda
7ac65e0cb75e7c2f121bbd4178675aae *data/reactome_descriptions.rda
76455f32ea75a2bcb79a5d0aa9867974 *data/reactome_genes.rda
8a5bfa944ee3d586085f05d7c2a24e81 *inst/CITATION
0e2d2bff299ff0b4501ac2ed2dd67924 *inst/doc/intro_vignette.R
8d200846b4e26134bffd80c0a66590f1 *inst/doc/intro_vignette.Rmd
2d5e4ecbc6e1344b8d35370fceb10e35 *inst/doc/intro_vignette.html
636efe51bd08bf1c29ddf72b66176c90 *inst/doc/manual_execution.R
5fbdffcb66f0599cebd2368324528959 *inst/doc/manual_execution.Rmd
edd97664af3d91771e9c18108355ba26 *inst/doc/manual_execution.html
e97b5819df2426c77eadec9550ce1056 *inst/doc/non_hs_analysis.R
a47b2fe0e0c917703a78702db0a64007 *inst/doc/non_hs_analysis.Rmd
8c941ce334db9b844c6a00dccf3359e7 *inst/doc/non_hs_analysis.html
45ee26db5b65613aceacb9e64733ee2f *inst/extdata/CREB.txt
aa1874ac25cbf1fcccbf8c3e3d9d6a9a *inst/extdata/MYC.txt
844bc1454577a688dde25aa0282c746c *inst/extdata/example_output-1.png
329f3582fd545de9b88e50b38da79650 *inst/extdata/logo.png
a0fe4a8f509b7b66597cd81db62944a7 *inst/extdata/resultActiveSubnetworkSearch.txt
89ea63d5ea6bb533fd447e8abdb024b4 *inst/java/ActiveSubnetworkSearch.jar
cd6cc32ef0ae5a3108bbb064d647bbb6 *inst/rmd/conversion_table.Rmd
7035b4a5b6fddac65a0ac4fe16990e37 *inst/rmd/enriched_terms.Rmd
4165bca20af768a694cd12a0b59b29b4 *inst/rmd/results.Rmd
5aefed1e6692c2d69686853966feb72d *java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
9732f3a20f8bfe3aae4a3182175cf9be *java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
3515d75b02366d82faf3ff152a63c95f *java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
c489bd5c01cf42e159e1ee3809ac3700 *java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
5e71444c2eba521fd96893f9cb200b87 *java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
f0aae5d87de27c5883efa7f10a4f0764 *java/ActiveSubnetworkSearchMisc/Gaussian.java
ea41691816e60d1b8ba2eb3755ffa69a *java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
b8cea43205699d2ced1cdac423e32baa *java/ActiveSubnetworkSearchMisc/Subnetwork.java
5577bdbec43ecfb930293c24a5c3ef2e *java/ActiveSubnetworkSearchMisc/ZStatistics.java
c8470b28cf601d3844eea0d13b2f912c *java/Application/AppActiveSubnetworkSearch.java
86f66bb7f7147c54fc21cb0daccdb446 *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
e1d373a1dbb53eacd4f1b5e3b41da747 *man/GO_all_terms_df.Rd
87eef2d3d30a519ed35562f684be36ea *man/RA_clustered.Rd
a7c739e7702e4ee307164b9ca7cd457e *man/RA_exp_mat.Rd
d493abc919f86ba0ded4f61edf78cddc *man/RA_input.Rd
605d1c82d7fab8c62437cf42380ae9c7 *man/RA_output.Rd
e36673090b6af083bf0ec3ebd64e895b *man/active_snw_search.Rd
61219babfca0f3658afa3a99625e351c *man/annotate_term_genes.Rd
3871034e3a479e71b1270c08c530f51c *man/biocarta_descriptions.Rd
757af6f81e7644e297522c6b9b72289f *man/biocarta_genes.Rd
6a98b8797bb5de007648c78f8ce1557f *man/biogrid_adj_list.Rd
e419d6e29bcd8c18b295ca0ec4b24cb2 *man/cluster_enriched_terms.Rd
84aa85f2a9ce92848b29872384d78dcc *man/cluster_graph_vis.Rd
52a9240879634da1a4163ee2f4c603e5 *man/color_kegg_pathway.Rd
bc553b4af1c44ad75048eee49a9c853f *man/create_kappa_matrix.Rd
6c30a16872b02e518ac5121088856a2f *man/custom_result.Rd
3b899fe234c9da82aa8410d0d4f9dade *man/enrichment.Rd
862d14705dd728758da596916ddd9f22 *man/enrichment_analyses.Rd
b468e1f7b21e9af363515f0d22aa56a8 *man/enrichment_chart.Rd
836858f733505e49377573a515dcb7a0 *man/example_active_snws.Rd
19afb77624872daed54cd36529036433 *man/fetch_gene_set.Rd
585cf0607163c0f7c20ab592bcf77e4e *man/filterActiveSnws.Rd
cd940a1866c0cc0f5cd08c73191e9e78 *man/fuzzy_term_clustering.Rd
9c0b55c14d56d9b964639af257b66514 *man/genemania_adj_list.Rd
535f8c6a35cd7de82ba2a46221936639 *man/go_all_genes.Rd
4d5b86dcd98b9b12077ddd4ce590aa6b *man/hierarchical_term_clustering.Rd
a4a7c92db45f8d6f6b1abcd5bc8e2364 *man/hyperg_test.Rd
10d631d1e8c71a9575f1762e7899acac *man/input_processing.Rd
45faf68570d11afa7e9f829be6420059 *man/input_testing.Rd
ebf2b24d861aa62b5d9065dcb9640592 *man/intact_adj_list.Rd
af78cd3ffb83bd1531887ecc22f51034 *man/kegg_adj_list.Rd
6c68b5960e055b60151e7575869fe4b2 *man/kegg_descriptions.Rd
401faac28dcae2adc39de7e212bc9761 *man/kegg_genes.Rd
4c32819a2881174ef16a8b63659af4fc *man/mmu_kegg_descriptions.Rd
fc6510c072100212c832d43e4729d363 *man/mmu_kegg_genes.Rd
56e872ae4557f54f976b97698a982160 *man/mmu_string_adj_list.Rd
bf14a7295df6fbe18c79d974ea48cb2e *man/myeloma_input.Rd
b38ffeee232bd776f83fc38ed49e64d2 *man/myeloma_output.Rd
fecfdb284440e0f9d88d17a510afe22b *man/pathfindR.Rd
9dc6218ad07294a518b33e60c41ea946 *man/plot_scores.Rd
101b84147fcb76d7dafe06a08908f57e *man/reactome_descriptions.Rd
0126f8f55509cdb397c5a912c49a9f21 *man/reactome_genes.Rd
9f6d5c0410c3326b95669be2a34aed45 *man/return_pin_path.Rd
19087ac8823e9c32cd5c3cd6f34da85e *man/run_pathfindR.Rd
c1e011ae3186dd4f6a45f89fda79075f *man/score_terms.Rd
aa2694bd3cf7c47593f7027270766708 *man/string_adj_list.Rd
6e235f4cbc5e99832c6a593074479788 *man/summarize_enrichment_results.Rd
e41457a545dab198accfc4b33f03b589 *man/term_gene_graph.Rd
faf7ee4029838319822efae2c0e8a14e *man/visualize_hsa_KEGG.Rd
1d42f30faff8b13dde0ac1ae9d0133c3 *man/visualize_term_interactions.Rd
8f8c4802a5f12155b39fa581dedfba60 *man/visualize_terms.Rd
89a515d1ab086e742a9aa71e910bffc6 *tests/testthat.R
4ed59864dbd89d020f11ca10bce58ac6 *tests/testthat/test-active_snw_functions.R
8c7a69093be3a81d113147f0ce015984 *tests/testthat/test-clustering_functions.R
e8ef4cd2aae7b3e9aca8221151818c3b *tests/testthat/test-core_functions.R
4ddd35a91eae61ef55b49c06426b21cd *tests/testthat/test-enrichment_functions.R
89d166a5fc58341328e3fb873bef1631 *tests/testthat/test-scoring.R
3a113f89c30f136f0d6d73073215bc1e *tests/testthat/test-visualization_functions.R
e0ded256aeea286bb001a9a89ca56fb5 *vignettes/example_interaction_vis.png
8d200846b4e26134bffd80c0a66590f1 *vignettes/intro_vignette.Rmd
157c5aa448fee542c18ad3314013b450 *vignettes/man_enrichment_chart.png
5fbdffcb66f0599cebd2368324528959 *vignettes/manual_execution.Rmd
a47b2fe0e0c917703a78702db0a64007 *vignettes/non_hs_analysis.Rmd
2e99533464a30126c1382db953397487 *vignettes/pathfindr.png
de8bae33cf62e8766ba986fbab02427e *vignettes/score_hmap.png
2b28501360bad9a8edd42daa83756854 *vignettes/term_clustering.png
4611e3e03e736f4193b8e431ae49144c *vignettes/term_gene.png
