8e4fbea2a07ba7b51321549510ca85ad *DESCRIPTION
93af81d069b8bba3212871bc420cc014 *INDEX
758d99e6ece1abf4f3e073aebae2e04c *Meta/Rd.rds
795ef1933dd6e5a92764af4150ef47ba *Meta/features.rds
0ccaabe00b1288c2ad318394a5bb2fcb *Meta/hsearch.rds
fd96993d90337ba552d41d0dc5ddc0a4 *Meta/links.rds
654df6e7154bb35f8bab9cc4eb660ac1 *Meta/nsInfo.rds
95c33c3b2d729a8c2421257f89e58dea *Meta/package.rds
8b0bae23c6004c137f3e6a3dc9775f77 *Meta/vignette.rds
0c0a6819ea26b862f6721fd92074b0d8 *NAMESPACE
d41d8cd98f00b204e9800998ecf8427e *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/trena
d63795c77629009cda46feff73939867 *R/trena.rdb
f14071d01e2c8e6d8559d013d913d33d *R/trena.rdx
90c0e8bfa2cf7ddd6468bd93728e0c4a *demos/Assess_Distributions.ipynb
d0f8ec216d6c5aa9c540a052384ded31 *demos/demoEnhancersDatabaseOnWhovian.R
7c46291e2d18d5c393cb0cb81a2c690e *demos/findPiez02RegulatorySnps.R
b963c9b3eeea35773d15e78140755fdc *demos/findTFs.R
568941e705e2d2e48d19fc8515c3a7ee *demos/runLassoSolver.R
f3f08b552e7b655835830eeee69808c6 *demos/test.png
7c1db56b0472c25a4c1bd94c36ffd586 *demos/trem2/go.R
bb06bf0fb67ea8aa2cea6aeebb64cb83 *doc/TReNA_Vignette.R
2758516fcd834a05d7a78c6df1780bc4 *doc/TReNA_Vignette.Rmd
ae0ba0f833c78a75f82304f4a4545aab *doc/TReNA_Vignette.html
3fb197ddb7614c84e97d72e1fdeb673d *doc/caseStudyFour.Rmd
7da2ba6492a6b3b31625ab174d68f44a *doc/caseStudyFour.html
4fd1d8b081e6dc7220047a5f28a340e8 *doc/caseStudyOne.Rmd
914ae1674c6e72bff4f71772187fbf49 *doc/caseStudyOne.html
28849001653153baf427835d053866ad *doc/caseStudyThree.Rmd
0bc067b42deeb3be0f99c84c3cde00b3 *doc/caseStudyThree.html
8a5e9b8eee276aca5826089f920ce294 *doc/caseStudyTwo.Rmd
1f5b25521fa2944a9d44c6f41e5a0756 *doc/caseStudyTwo.html
84a023196ec76269df0aba5573f31521 *doc/index.html
a9a761a4d2e2da80038ae43e5810e1e7 *doc/overview.R
00bcad4b23d28942d8534bd9d672075e *doc/overview.Rmd
2d2208255667907b02874877375954a6 *doc/overview.html
1981372d208254872c58de7241892983 *doc/simple.R
7fc36e9b56a4f55afe5c2468c6599240 *doc/simple.Rmd
966e900d73560cfc377e775634cf2d15 *doc/simple.html
d9630875010da97101e61b7cdf8c8f67 *doc/tiny.R
05dc3d6c13ed0e1ffbc845ac43c3c936 *doc/tiny.Rmd
2abd83dec7995d00cc6d1ed87a5f62af *doc/tiny.html
55f2fbcdca4a18aa169b1d32bacadf25 *extdata/all_motifs.meme
4210742ee291565ffb4dcff88f735231 *extdata/ampAD.154genes.mef2cTFs.278samples.RData
dbead999a8d9f52a1333a83c9820b25f *extdata/ampAD.58genes.mef2cTFs.278samples.RData
d87b217981d6637177dd7ef89285d45e *extdata/brand.tbl.model.trimmed.RData
1a07499c5ce7cb687bb3afa7212711ed *extdata/human.regulatory.genes.RData
8599edf9f31e819ec9930cb925d3f89b *extdata/mef2c.neigborhood.hg38.footprints.db
dae3572ee80040f26811a88e558aafa1 *extdata/mef2c.neighborhood.hg38.gtfAnnotation.db
07159b29ce16bc75ad719cf06ea6aef7 *extdata/tbl.mef2c.model.RData
2f431edaf8b630f45390b4a6b772985c *extdata/vrk2.neigborhood.hg38.footprints.db
9cc8f2194355bff535d157549af9f183 *extdata/vrk2.neighborhood.hg38.gtfAnnotation.db
e715b1a24c2a8f0ed1dfac4202423d28 *extdata/xgboost.sample.RData
e942c1e6fe9136e3008fc2191a4ec77b *extdata/yeast-53genes-536-samples.RData
c5657a9d9af48f9fd3ca7b94a4fbb730 *help/AnIndex
ad9c22b0333efe0ab85d705e4de1a282 *help/aliases.rds
9e2fa39e745510fce7f67efab1d26909 *help/paths.rds
8b0997877ae50922985d9bd5b746de30 *help/trena.rdb
f3eb0afeaeac99ca5bb69690da4daf59 *help/trena.rdx
e1f5324a89019332e5bfefc175cb27b7 *html/00Index.html
3845aef6126cf18c45937f292f23508c *html/R.css
68b329da9893e34099c7d8ad5cb9c940 *misc/assessSnp.R
5044331f65d1b794c79823478f348a4d *misc/createSQLiteDB.R
49dd7794824f19fffead817eed129895 *misc/footprintFinding/piq/makefile
6f962e99ba3a23ec481825bfcf7a32bb *misc/makeTRN-proximalanddistal-demo.R
e144e6dba9d76f1b04b750da054ecb8b *misc/makeTRN-proximalonly-demo.R
0d84813f34a485b92f0f52fdaee06f9c *misc/monteCarloTRN.R
ec85a10a40cfb67e87d28016a07c9ee4 *misc/multiModels/aqp4-multi.R
a058f7ae064b5aa02384d2f25ffccaf2 *misc/multiModels/aqp4.R
ef215e2597fabe5491abeeed88a2dc25 *misc/multiModels/graphToJSON-devel.R
7b6e81ed9ee151e7cdbc5d2e670895d5 *misc/multiModels/style.js
8379f576fb8b820a736fa10d92870ca9 *misc/profileDbQueries.R
dcfd3fb17c5cf72305bd02cf22c14004 *misc/runTReNA-demo.R
7be14cd38bf61ba16f2339fe39b440e9 *notes/fillEnhancerDatabase.txt
3a1f2b5e74bd8ec4c2a369172e6e4944 *unitTests/bugDemo001.R
522a5f9ef4390d0d14f4163800cf20b7 *unitTests/hidden_PCAMax.R
7a986ed01ae12f72457f1ce7d4bbd49d *unitTests/noTest_Trena.R-hidden
b10a420df4e7edf977aa74608e879faf *unitTests/tbl.snps.RData
a5d2bdeccd9851ab528225ccd047b9e0 *unitTests/test_BicorSolver.R
d7572d9d4166a897aebd7f11ded7eb52 *unitTests/test_CandidateFilter.R
035676e6ed46d93102f2864619c1b0b9 *unitTests/test_EnsembleSolver.R
7d78abe8460109297188120dc5e1d329 *unitTests/test_FootprintFilter.R
93cf76cc6ff942bdb6534a3b8c9e68a8 *unitTests/test_FootprintFinder.R
d216c9bfb790faead71948c2a235ab44 *unitTests/test_GeneOntologyFilter.R
758e2522660cdfe4d5a4cd27274aee1f *unitTests/test_HumanDHSFilter.R
bec13922a717cdeeca81349a63362331 *unitTests/test_LassoPVSolver.R
9e427196604e092e0e85db11be407e0c *unitTests/test_LassoSolver.R
0c8b8edaa37ae9d0dd66502309123a3c *unitTests/test_MotifMatcher.R
80cf666d91c45d2cfda966ee50498ebe *unitTests/test_PearsonSolver.R
456c1bd048c27b4744e583260dafbb8b *unitTests/test_RandomForestSolver.R
7084cd4dd99018e18d880aa4480cc599 *unitTests/test_RidgeSolver.R
fbe7f14a402cbc2265add322e1749ab4 *unitTests/test_Solver.R
f43cf1407d9ccb3b98cd88bc3fe34cb5 *unitTests/test_SpearmanSolver.R
1fa0d3cb87a0a3fcf9b8f5b4f511dc23 *unitTests/test_VarianceFilter.R
08d2f2974fcc8e2f20d32581b178c3bd *unitTests/test_XGBoostSolver.R
d3dcc060dfeec38a7bdadd57fbb5f240 *utils/NaiveSolver.R
dd9e6dba8a5c90b75ece66b3331d29aa *utils/TReNA.R
8349495ac8d9523ed3406b1fa21ca319 *utils/additionalTReNATests.R
9650189a5236a77e62a563cae12b5b01 *utils/createGenomeScaleModel.R
ba2d423aa4aaab6877be89b13562cff9 *utils/createGlobusTable.R
873ef9e83a4cb67a158ef09601678a23 *utils/currentDBs.html
ab691993403cf6bb6702e5c61277d37b *utils/determineSqrtLambda.R
46aad2b54f64c04cacdfc9471c70127b *utils/evaluateAllSolvers.R
8bf84364e45060a1e4a4a77f68da9c07 *utils/extraFunctions.R
8e0cdefe1df4a74c1fba812d0f563dad *utils/runTReNA.R
380c5331c759be0cf1b15cdb5788845f *utils/test_NaiveSolver.R
c3abc15e40ab1f23ded844d454f8de2f *utils/test_TReNA.R
187c3d72fa9e8de13ed98e58da1d384d *utils/test_runTReNA.R
