709609df24106dc7c571bfacb8bbb2d0 *DESCRIPTION
637e88461df3e5b7224845189cb3f31d *LICENSE
62cbea5c6433f8d94366a9a390063161 *NAMESPACE
bd60301bd852ed67f945b85be18604c2 *NEWS.md
3e02052a9b5ee54668a002e86fe23d53 *R/data.R
b71e2be0d4ba3f790b13b87246be4588 *R/enrichment.R
a0d7f7e6f4f315bf951fa64ee6a27810 *R/input_processing.R
0fa97406f89fe7f3246d4525ac053e83 *R/parseActive.R
d92b472702dcdcee964918062aaae357 *R/pathfindR.R
7e676603d1337ce2f3218d8a1f946751 *R/pathmap.R
6272788cdaac727f5b82652eabdf4f43 *R/pwd.R
341688e609020a8b3748cb11c8364f62 *R/scores.R
1c27988a41c25e0cfec4e4d83681de87 *R/wrapper.R
da167ba90e00e03d3af155f2e16d49c6 *build/vignette.rds
ade71ffa9d62f38b4c97320ea5999fce *data/RA_clustered.rda
802cfde2f633f4b83e4d420ae89eb6cb *data/RA_exp_mat.rda
45d3c9fc8c70d89595f65875e5f983a2 *data/RA_input.rda
a152d2cb0a4560265fb60ce82412416e *data/RA_output.rda
d311f907f99b95103c9e80dc7ab16b53 *data/biocarta_genes.rda
07530d05a1d8b6d5b12b0ed995ccbeb4 *data/biocarta_pathways.rda
7427188e7f17a6c37abbfe85a3b21f61 *data/custom_result.rda
7eef290585c63100c2245d73d6069060 *data/go_bp_genes.rda
2c8dfe82aaac60ed996ba7ea8c975323 *data/go_bp_pathways.rda
af923135a925f7e85169b0b7f9495a6e *data/go_cc_genes.rda
d1f8269113684b179b26fc48bf4c71de *data/go_cc_pathways.rda
11ab7ec716907decc2c14cc8b4b05161 *data/go_mf_genes.rda
ee930b376c0f1aa755d0f3bb4b342183 *data/go_mf_pathways.rda
488a984e0faa67204bf1b6a91fe01f48 *data/kegg_genes.rda
015c9826df383d727432d141eb076c7d *data/kegg_pathways.rda
c06ac5d36c6ae98eb8fd79fad6cd2f9c *data/reactome_genes.rda
e13b8c35d084794bf9695d3dde0aad19 *data/reactome_pathways.rda
759ff6a955637632be9f38df89ea7abe *inst/CITATION
72e3931beb3ca3dc5890104705bdd7c3 *inst/doc/pathfindr_vignette.R
bb58480b50af89467c8633df02c6c6df *inst/doc/pathfindr_vignette.Rmd
c06ee0ae90127faac14ad5eb933a1d79 *inst/doc/pathfindr_vignette.html
9b65fa19fd39f1149773f43320a6b715 *inst/extdata/Biogrid.sif
679f1c8084e7d30a0dc81709e514298a *inst/extdata/CREB.txt
c804db2e6802b505a35236621f393543 *inst/extdata/GeneMania.sif
7d1a2a950fa4f1d00af771b59388c804 *inst/extdata/IntAct.sif
3e8182b384b72c96124777f48102d274 *inst/extdata/KEGG.sif
4f97ce8df0d7dbfa3746e3192c639596 *inst/extdata/MYC.txt
a23abda2700faa198d10b4ad270fedee *inst/extdata/resultActiveSubnetworkSearch.txt
a7c259ca331087f1923fec34d2153a36 *inst/java/ActiveSubnetworkSearch.jar
cba4610f9829147243902e3dcc6cf402 *inst/rmd/all_pathways.Rmd
457a2ab4fae3c6997bd04b1d004a6e42 *inst/rmd/clustering.Rmd
95aeb566f824d32e44dd00c3b63a8405 *inst/rmd/genes_table.Rmd
d2c85e126b09897374c0cf403903ef95 *inst/rmd/results.Rmd
5aefed1e6692c2d69686853966feb72d *java/ActiveSubnetworkSearchAlgorithms/ActiveSubnetworkSearch.java
e1add96c381119ca5c12a4d5ef19f031 *java/ActiveSubnetworkSearchAlgorithms/GAIndividual.java
4fc331bf185741e6851c5f9bba4f1a77 *java/ActiveSubnetworkSearchAlgorithms/GeneticAlgorithm.java
c489bd5c01cf42e159e1ee3809ac3700 *java/ActiveSubnetworkSearchAlgorithms/GreedySearch.java
5e71444c2eba521fd96893f9cb200b87 *java/ActiveSubnetworkSearchAlgorithms/SimulatedAnnealing.java
f0aae5d87de27c5883efa7f10a4f0764 *java/ActiveSubnetworkSearchMisc/Gaussian.java
1de145f422767954ae5000541addf3a2 *java/ActiveSubnetworkSearchMisc/ScoreCalculations.java
b8cea43205699d2ced1cdac423e32baa *java/ActiveSubnetworkSearchMisc/Subnetwork.java
5577bdbec43ecfb930293c24a5c3ef2e *java/ActiveSubnetworkSearchMisc/ZStatistics.java
9e607a52c81e197f7ab1025b5a3202b1 *java/Application/AppActiveSubnetworkSearch.java
ee4bd21bb3909f75dce8cd63c620b483 *java/Application/Parameters.java
d4315317f84edad39baa6d6ffba98b50 *java/File/ExperimentFileReader.java
4d004757ba404d6c16b73bfbaff9fef9 *java/File/SIFReader.java
91ad54d743857dd002a704cf50159e0d *java/Network/Network.java
f516e3c30a9953abaf0f48ab54de9a9e *java/Network/Node.java
fb9a95c51d77dbb3580f57c63c9582ea *java/Network/SubnetworkFinder.java
59274f0e62f0765c50b5b51546e0a240 *man/RA_clustered.Rd
6d2465eae28af7f1a815aea25087ab40 *man/RA_exp_mat.Rd
524e7829e440c240cd165347eb2fd6a8 *man/RA_input.Rd
dd4c48ab4295401f66340bb3b491c6bd *man/RA_output.Rd
387abe02f6effe6ad385e2a23406cf6a *man/biocarta_genes.Rd
6350c2b26a7f2ddbc7b95ea417f4a433 *man/biocarta_pathways.Rd
70163fa910f129536e151a336c17ab79 *man/calculate_pw_scores.Rd
c89b0cb1d62a773884ad7c43f4c42a75 *man/calculate_pwd.Rd
5aee91bb33c5e493df83b32038163732 *man/choose_clusters.Rd
2fe9270c47eda5426ec46e5e0d3582cd *man/custom_result.Rd
43abab1f14ff0669196ab4b75c2d92ed *man/enrichment.Rd
9a97e1f0611e4dde1078cf87cfbb6e2c *man/enrichment_chart.Rd
047fd377f9600e3fd8954fd8927b5776 *man/go_bp_genes.Rd
1148a0ed0f2e1bbac2615e6164908065 *man/go_bp_pathways.Rd
8bd76eda6e6414975fdd22e67e3a58bc *man/go_cc_genes.Rd
04f61793d1efc0c10170bd0419909fba *man/go_cc_pathways.Rd
5829b330d157fe3b730bfcaaf9d4656b *man/go_mf_genes.Rd
2ce039a78afc16e9aaa4ac13c2546dfb *man/go_mf_pathways.Rd
b9e03051994c62dd48a4d35ad5293565 *man/input_processing.Rd
a06e9d7d2c44bf4f8a13a09b176ff0f4 *man/input_testing.Rd
c69d78fc2a2fceba75de2c4f8abe9c60 *man/kegg_genes.Rd
c84285a998f040086886a5a2728e1a4b *man/kegg_pathways.Rd
c81afafb03343b34c00c121fedecae04 *man/parseActiveSnwSearch.Rd
fe1eb71a86819302ba960d10f0ef9f0d *man/pathfindR.Rd
134321777b4ffecd4547af36f59678e1 *man/pathmap.Rd
fa14c4b6d4705236c0f7ad4f3406d0bd *man/plot_scores.Rd
6084c4eb5b137df4955b80cbe97a5b59 *man/reactome_genes.Rd
cb4ec25a1f22de1bbfeb7bcbdf26d79c *man/reactome_pathways.Rd
eefdfc14dd06ccbc55da9aaf41b6ef4f *man/return_pin_path.Rd
f31fbe3a9c9e24a27978d4843f1563ac *man/run_pathfindR.Rd
b4d99d5c04387ff6266ebf16d90269eb *vignettes/pathfindr.png
bb58480b50af89467c8633df02c6c6df *vignettes/pathfindr_vignette.Rmd
cc244c57d2cd0332d5fa04dbbc3475e8 *vignettes/pw_clustering.png
b4011af00a8d671bf049aa9e1e46bdd1 *vignettes/pw_score_hmap.png
