28738b079840fb07acae3a2dad75cdc6 *DESCRIPTION
f93c9195970d0d3a884265228e8dc18c *INDEX
a4cf07720e3c63d52bd34a0a6697b57a *LICENSE
9b3834c08c4f9a3a2c903e14a56078ff *Meta/Rd.rds
c8440c06be5e093e05779d74c0ffa6b7 *Meta/features.rds
b87335b2e4efafdc9bae118f3100280e *Meta/hsearch.rds
1838be8e634e9acdc0f0d20574e674a3 *Meta/links.rds
ea5af22c104377bfda8ab9dba76a142b *Meta/nsInfo.rds
faec96e89bfbe2a5ad1e0e19c271ea95 *Meta/package.rds
4cf475501d212d50e90ab52aae7dcee9 *Meta/vignette.rds
10097d722c404fb0543932efe6f588e6 *NAMESPACE
c07a76930761297f4530785bfc5ba65d *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/TraRe
8d640964b415bdb92257b83f64143692 *R/TraRe.rdb
afa9f528057f5373920fac71df2e6166 *R/TraRe.rdx
22ae7fe4fdc23efc35fd1fe1fca5370b *doc/TraRe.R
a20450ecb75a1c44bbd9a8edb39472d2 *doc/TraRe.Rmd
843faf38a64651435c3fff5236df6356 *doc/TraRe.html
918cfa01b15d5880ad708142e79b9668 *doc/index.html
356ddb73c2ac690b9ab039f3f35df653 *extdata/ChIP/Tumor_OV50.gene_info.txt
9bf85b855c2c54457d802628362bc0ff *extdata/ChIP/Tumor_OV50.tar8855_reg638.VBSR.m100_b10.rds
2ef001e44e17a44c32c510257029bd5c *extdata/ChIP/Tumor_OV50_intersectBed.weighted_evidence.txt
031753f4bae2272b65615068845b5b02 *extdata/RewiringReport/glossary.txt
b103eb1265a62f9f6a7ebf7519891ce7 *extdata/RewiringReport/sorttable.js
2b33942bb844a1d669bdae88f14de31e *extdata/VignetteFiles/SEObject.rds
f13b015515e2503642d0196b040a047a *extdata/VignetteFiles/expression_rewiring_vignette.txt
83e71a16bdf315f5d053846489a64192 *extdata/VignetteFiles/graph_netrun_vignette.rds
93e3b1eff75aa01dfb0bae6a013fc8b7 *extdata/VignetteFiles/linker_output_vignette.rds
a4a1e736b049091c9496d183a925ac97 *extdata/expression_rewiring_example.txt
26a37cd3890484531d481fffffb3f3bd *extdata/geneinfo_rewiring_example.txt
47d268bf6ef094295acd01bd3f99bc56 *extdata/graph_netrun_example.rds
1554a508b3e1fd6ae3764b3d72b74393 *extdata/linker_phaseone_example.rds
61aec8fd4f6ece651beedebdbaa416d6 *extdata/linker_rewiring_example.rds
40879836fdc5079fdfe9c0c008958f34 *extdata/phenotype_rewiring_example.txt
dfb486d919e1243e2934a2823e03c405 *extdata/prepared_rewiring_example.rds
20a9a7f2eccb33e104acfb3c54b051e5 *extdata/refinedsumm.rds
a9aff9d3318a832c4d0409ed5f1d86a9 *extdata/targets_linker_example.rds
a22b79331afe80c209f6eade1ffd945d *extdata/tfs_linker_example.rds
bed35f7351264be724342b423b2bbec8 *extdata/tfs_linker_example_eg.rds
89773eee2416e1182769b9174cb47e65 *help/AnIndex
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_EvaluateTestSet.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_LearnRegulatoryPrograms.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_ReassignGenesToClusters.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_corrClust.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_extract_modules.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_init.html
b878598e9fe90ecb2c810e9dd215b509 *help/LINKER_run.html
4ab01d7675126f029087ff8b8c64c5e8 *help/LINKER_runPhase1.html
f079315af72f94dc33a0038fca8366d8 *help/LINKER_runPhase2.html
e1cc5af45b0366c0ba55ffe670575108 *help/NET_compute_graph_all_LASSO1se.html
e1cc5af45b0366c0ba55ffe670575108 *help/NET_compute_graph_all_LASSOmin.html
e1cc5af45b0366c0ba55ffe670575108 *help/NET_compute_graph_all_LM.html
e1cc5af45b0366c0ba55ffe670575108 *help/NET_compute_graph_all_VBSR.html
e1cc5af45b0366c0ba55ffe670575108 *help/NET_run.html
29bdd2dd736c35e320db8ee51a24fa19 *help/TraRe-package.html
29bdd2dd736c35e320db8ee51a24fa19 *help/TraRe.html
23d16247c03456b757e29d76496aed48 *help/TraRe.rdb
fb0fe44bf978738df2945f8a60846688 *help/TraRe.rdx
ca2ad84086878e82808647a75f68e0eb *help/aliases.rds
b699d9636574948762d9fc17805f9b2b *help/create_html_summary.html
81bc4a04e106d2f947fc3bbb73600d2d *help/generatecliques.html
81bc4a04e106d2f947fc3bbb73600d2d *help/generategraph.html
61b069645e99b846adec16ec742a2ecf *help/html_from_graph.html
865e1fba717f1fdea663fa0e6e48b027 *help/orderGraphWeights.html
b9f231a8c552268ec28d8e8d5bef17bc *help/paths.rds
865e1fba717f1fdea663fa0e6e48b027 *help/plot_igraph.html
81bc4a04e106d2f947fc3bbb73600d2d *help/plotcliques.html
81bc4a04e106d2f947fc3bbb73600d2d *help/preparedata.html
2d7ebc7cfe61fe01f23dc3fa26abf309 *help/preparerewiring.html
865e1fba717f1fdea663fa0e6e48b027 *help/return_layout.html
865e1fba717f1fdea663fa0e6e48b027 *help/return_layout_phenotype.html
4f7a4919c23d0bae57c0a6a84becd883 *help/rewiring_test.html
4f7a4919c23d0bae57c0a6a84becd883 *help/rewiring_test_pair_detail.html
6c1c0f40789e8e865544175bb374a900 *help/runrewiring.html
81bc4a04e106d2f947fc3bbb73600d2d *help/selectmethod.html
d22e399a3766237384523c87353ab851 *html/00Index.html
a1199a93b5114866036280183c088bcc *html/LINKER_run.html
ca2a8efe7740e4de4afa321e921dd07e *html/LINKER_runPhase1.html
b27e2381212e0a8984b535f73885d25a *html/LINKER_runPhase2.html
244bb208f31ae25cbfaeb350f9bf804a *html/NET_run.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
dc86f2a6ade0edb80da64af8015032ae *html/TraRe.html
28b5566ad9fc2dec927da8bb09d6b3cc *html/create_html_summary.html
15c6bab7250aebcadcbc50877e7d7d63 *html/generatecliques.html
f7435016043d2a3bccc5ed17212a27d9 *html/html_from_graph.html
0c9077c5765a6a69452c956c66c6f111 *html/plot_igraph.html
4fd4e338b7f461cdd0394541c5305698 *html/preparerewiring.html
50bea8a597c411986c0829976716d212 *html/rewiring_test.html
3cb24a402d9cdb77db59b6de3ffc319c *html/runrewiring.html
1fc03a6d6bc49f097ec72fcd324f3b24 *unitTests/cliquesgeneration_tests.R
0b3f2c8a8707449a27882ebc28f9a3a8 *unitTests/excel_generation_tests.R
517507c9151451db914324591a2e236a *unitTests/plot_tests.R
f6ae3fda374fb39f7b9d162189183de5 *unitTests/rewiring_tests.R
a159a0cb3beae7cec46064ffcb5f4535 *unitTests/runlinker_testindex.R
364161ce32e5fa44c00a175571b0658c *unitTests/runlinker_testmatrix.R
dfded7e72e272d813320a5d16650f1a3 *unitTests/runlinkernet_testindex.R
523c028ac6e98157363f7ea1685ee73f *unitTests/runlinkernet_testmatrix.R
