ca3b60e3b5716da95769d5a469c18c77 *DESCRIPTION
f93c9195970d0d3a884265228e8dc18c *INDEX
a4cf07720e3c63d52bd34a0a6697b57a *LICENSE
16c9d27cbc72d71ad212cd0c22cf27c7 *Meta/Rd.rds
8503e676975364d771072956cdbca633 *Meta/features.rds
dd50848b1ea9946d218fc404dd7166c9 *Meta/hsearch.rds
8ffe6f7651b974841fb0efb7e4a70c85 *Meta/links.rds
35d3c52338aa41070a3a9fe710cd1685 *Meta/nsInfo.rds
4a772a5066e09762a618fbe5d7d40347 *Meta/package.rds
3cf64732c7b1ca792fa4e393d05530cf *Meta/vignette.rds
10097d722c404fb0543932efe6f588e6 *NAMESPACE
c07a76930761297f4530785bfc5ba65d *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/TraRe
b375d67d495f8855b86e392e866e876d *R/TraRe.rdb
f1df461d781278ea568c04bf81515a3a *R/TraRe.rdx
22ae7fe4fdc23efc35fd1fe1fca5370b *doc/TraRe.R
a20450ecb75a1c44bbd9a8edb39472d2 *doc/TraRe.Rmd
36c8ca02834b1f00276b64bd7cefdfc2 *doc/TraRe.html
8cdc19b4c81a22b43dbdd4dbb0727bc4 *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
6b683918df1654d40b0cff5868a15946 *help/TraRe.rdb
20c61f731996158fb977aeb4e2650a52 *help/TraRe.rdx
074e0828f731b4fb5e708a8678168ecb *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
5556a2457f5f41663fcb69fe65e4ac54 *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
2fbdf0e01d611d2cb3aadf4df3782703 *html/00Index.html
6bdc50079a65a0b16013951ceb9f6a8d *html/LINKER_run.html
7f867c2207b41d121a4e8be98d902140 *html/LINKER_runPhase1.html
5ae65e3096ffa3ab5ba692705b10a382 *html/LINKER_runPhase2.html
a61509c6074d5efc1e13858e4e68165b *html/NET_run.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
857e8ab0208b410b19e7463d4d5d05a0 *html/TraRe.html
7397d55f5cfac298729dad60e82ab646 *html/create_html_summary.html
120d731dc39ed92a4bd5902c6d05d289 *html/generatecliques.html
c6dcb840227ce4a8e85746d2cc51af0f *html/html_from_graph.html
04fbad60a2a41bc8ea7647c2e65b7c2e *html/plot_igraph.html
22737e0047213318af63e9ee00566508 *html/preparerewiring.html
9e2086c1d7ef49753d9e2a74f7c18191 *html/rewiring_test.html
9bb0314334ff8ed63bc4ed56d438abe8 *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
