55522dcf8aa4832fd98d4fc52d183229 *DESCRIPTION
75e6f4e9231deba70a15735cb69ebf10 *INDEX
ebc5d2f1a67f7d713dd68c112667b04c *Meta/Rd.rds
c8440c06be5e093e05779d74c0ffa6b7 *Meta/features.rds
cba73f36aaffa2d35a26de229eab5d90 *Meta/hsearch.rds
26d0695ec53204e2b9dfd74e7b00599d *Meta/links.rds
547c13eb21efd9eaaa9e696d8f271cd9 *Meta/nsInfo.rds
ee39c2a3abc83110e10b706245239230 *Meta/package.rds
cab3c551922c42977349cdc51a77e361 *Meta/vignette.rds
c75140b8005372890c8521a1c4a6a90d *NAMESPACE
d41d8cd98f00b204e9800998ecf8427e *NEWS
d6c68f1fe41ced6e98a766a3757313da *R/trena
4a14437042f985aabb9f26d69ee2022b *R/trena.rdb
459373c8e8ca5241ab93898b30d72321 *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
e6e3931cdf343b6495fe1ffb0e3791e4 *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
4e135e6afaadecec9f833b4cbf4f9be3 *doc/index.html
86c972d2fd391f25e59a42f4caeaa99b *doc/overview.R
88fddb55e5321a899ec069f97693c4ee *doc/overview.Rmd
40f6bfc5cc8acafd670ff5a528971bed *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
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
c189a21b6c7dd466eaca461d53e77272 *help/AnIndex
e301b7a4380a388c1e8363aef2127067 *help/BayesSpikeSolver-class.html
5b33c9cfa2e16e43f6503d3301bf1cc3 *help/BayesSpikeSolver.html
37e8a893e784f16c3a20c79301255152 *help/CandidateFilter-class.html
37e8a893e784f16c3a20c79301255152 *help/CandidateFilter.html
a3a7bc818d6853fde576fd4ee134a13e *help/EnsembleSolver-class.html
0d2a26caa96143b0f2ed31ad3f6218ea *help/EnsembleSolver.html
9400190415a718f29e9372029b249ea4 *help/FootprintFilter-class.html
9400190415a718f29e9372029b249ea4 *help/FootprintFilter.html
01d7c4167c94c93c1fcb7a3ff21cd0a1 *help/FootprintFinder-class.html
01d7c4167c94c93c1fcb7a3ff21cd0a1 *help/FootprintFinder.html
40a4c2a413432b8d3c547dc4489abc33 *help/GeneOntologyFilter-class.html
40a4c2a413432b8d3c547dc4489abc33 *help/GeneOntologyFilter.html
cd5a4954fb764f210609867efe381b98 *help/HumanDHSFilter-class.html
cd5a4954fb764f210609867efe381b98 *help/HumanDHSFilter.html
392961ccd63cb37207064fc0ac8327ef *help/LassoPVSolver-class.html
c82193ceef47a09403f3d46577a5c7c2 *help/LassoPVSolver.html
b8981d7667648bd7ef06e806d9e64324 *help/LassoSolver-class.html
a1401a67d72f8ec487b8b10fdbc72010 *help/LassoSolver.html
9b35e34831f21c4728f5e86acfcccb88 *help/MotifMatcher-class.html
9b35e34831f21c4728f5e86acfcccb88 *help/MotifMatcher.html
30b4d84479d1415d3d7422e65f508f3c *help/PCAMax.html
1170d6a6eb7eb0f4e3e3d7fad756a797 *help/PearsonSolver-class.html
a1814a64e699cf3a72c0b95f3d965fe8 *help/PearsonSolver.html
4ecac661131d20c8be114b8827222767 *help/RandomForestSolver-class.html
d0a5364afd5b49cff6f3223e39f713e6 *help/RandomForestSolver.html
fbcfbaaa4e7c6ba3d47550a7a5231bb7 *help/RidgeSolver-class.html
8ed49fe82a5a057f4ba318e70a04d50c *help/RidgeSolver.html
d54f88da1d54e8e2b102119c2c15e5d9 *help/Solver-class.html
d54f88da1d54e8e2b102119c2c15e5d9 *help/Solver.html
10883f407ff1c633bbff8b21826add9e *help/SpearmanSolver-class.html
332d4b671e838e3cf22c2a88147c0534 *help/SpearmanSolver.html
b4f48a42aeb2984f5b132851ac51f4e0 *help/Trena-class.html
b4f48a42aeb2984f5b132851ac51f4e0 *help/Trena.html
55838e004a3c51d9d3b44445c4a8c6e6 *help/VarianceFilter-class.html
55838e004a3c51d9d3b44445c4a8c6e6 *help/VarianceFilter.html
d7c0b076095c8983fbf4c73fdc8ec750 *help/XGBoostSolver-class.html
a89ff4a3e1704622fb7a2186a81feead *help/XGBoostSolver.html
a0953ec0d6497b5b0e913d5f003c5728 *help/addStats,PCAMax-method.html
a0953ec0d6497b5b0e913d5f003c5728 *help/addStats.html
fa0c439c24dcf46c86ad3badafa0bf5b *help/addStatsSimple,PCAMax-method.html
fa0c439c24dcf46c86ad3badafa0bf5b *help/addStatsSimple.html
572e5d9c2c5b33401ccfc7d59d76bc54 *help/aliases.rds
d679910041033446fadb70e0d8b6b196 *help/assessSnp,Trena-method.html
d679910041033446fadb70e0d8b6b196 *help/assessSnp.html
8dcf66aa9e1884f9f82d391b37cf4741 *help/closeDatabaseConnections,FootprintFinder-method.html
8dcf66aa9e1884f9f82d391b37cf4741 *help/closeDatabaseConnections.html
cf33eb694c7e98b074524521ea8cba9e *help/createGeneModelFromRegulatoryRegions,Trena-method.html
cf33eb694c7e98b074524521ea8cba9e *help/createGeneModelFromRegulatoryRegions.html
65c5cc66763e2a2b28d6875544a7897c *help/createGeneModelFromTfList,Trena-method.html
65c5cc66763e2a2b28d6875544a7897c *help/createGeneModelFromTfList.html
da11c1bbab94686875d9e09a0d92258a *help/elasticNetSolver.html
7b4180fd460dbb805c45538f81614a99 *help/findMatchesByChromosomalRegion,MotifMatcher-method.html
7b4180fd460dbb805c45538f81614a99 *help/findMatchesByChromosomalRegion.html
dd507bc72047cbefda9442bac78d6449 *help/getAssayData,Solver-method.html
dd507bc72047cbefda9442bac78d6449 *help/getAssayData.html
42909945770ab700923cb85abeeb4649 *help/getAvailableSolvers.html
7c777c0617c8cdd0ee433f27c7c73523 *help/getCandidates,FootprintFilter-method.html
695afe7d68f3219dff08dc973e99fff1 *help/getCandidates,GeneOntologyFilter-method.html
d54159b929848210718431938a942422 *help/getCandidates,HumanDHSFilter-method.html
8f3d793af130e9e474ce50d0983eefff *help/getCandidates,VarianceFilter-method.html
7c777c0617c8cdd0ee433f27c7c73523 *help/getCandidates-FootprintFilter-method.html
7c777c0617c8cdd0ee433f27c7c73523 *help/getCandidates-FootprintFilter.html
695afe7d68f3219dff08dc973e99fff1 *help/getCandidates-GeneOntologyFilter-method.html
695afe7d68f3219dff08dc973e99fff1 *help/getCandidates-GeneOntologyFilter.html
d54159b929848210718431938a942422 *help/getCandidates-HumanDHSFilter-method.html
d54159b929848210718431938a942422 *help/getCandidates-HumanDHSFilter.html
8f3d793af130e9e474ce50d0983eefff *help/getCandidates-VarianceFilter-method.html
8f3d793af130e9e474ce50d0983eefff *help/getCandidates-VarianceFilter.html
fdcb49527e99b4fba770733c43c9e9de *help/getCandidates.html
c05e4055f607c3988ccdf7aee6f0c309 *help/getChromLoc,FootprintFinder-method.html
c05e4055f607c3988ccdf7aee6f0c309 *help/getChromLoc.html
3b77c74105facb00db9b7fd079a1637e *help/getCoverage,PCAMax-method.html
3b77c74105facb00db9b7fd079a1637e *help/getCoverage.html
41a21c66e46d98850225c1959738a7df *help/getEncodeRegulatoryTableNames,HumanDHSFilter-method.html
41a21c66e46d98850225c1959738a7df *help/getEncodeRegulatoryTableNames-HumanDHSFilter.html
41a21c66e46d98850225c1959738a7df *help/getEncodeRegulatoryTableNames.html
a8ae7be711180a3cca58fe159e50ff5e *help/getFootprintsForGene,FootprintFinder-method.html
a8ae7be711180a3cca58fe159e50ff5e *help/getFootprintsForGene.html
0113e43842ad9db858daabf63bc79b99 *help/getFootprintsInRegion,FootprintFinder-method.html
0113e43842ad9db858daabf63bc79b99 *help/getFootprintsInRegion.html
4008aaf382848114cf73c166b41f770e *help/getGeneModelTableColumnNames,Trena-method.html
4008aaf382848114cf73c166b41f770e *help/getGeneModelTableColumnNames.html
8371f7d4a7d8427f086f6297de5e4e31 *help/getGenePromoterRegion,FootprintFinder-method.html
8371f7d4a7d8427f086f6297de5e4e31 *help/getGenePromoterRegion.html
7a01d0b803fe2c77f1a569cc28e2a3b7 *help/getGtfGeneBioTypes,FootprintFinder-method.html
7a01d0b803fe2c77f1a569cc28e2a3b7 *help/getGtfGeneBioTypes.html
7f5eb2a3b9d8912739e2b4111942923f *help/getGtfMoleculeTypes,FootprintFinder-method.html
7f5eb2a3b9d8912739e2b4111942923f *help/getGtfMoleculeTypes.html
2aab73e8f407fefb8ece5e2ee4ca2b94 *help/getPfms,MotifMatcher-method.html
2aab73e8f407fefb8ece5e2ee4ca2b94 *help/getPfms.html
2ac5fd5276d27873f527ddacb81427d8 *help/getPromoterRegionsAllGenes,FootprintFinder-method.html
2ac5fd5276d27873f527ddacb81427d8 *help/getPromoterRegionsAllGenes.html
c739c21bb9eb938f5c15f4a67b212a04 *help/getProximalPromoter,Trena-method.html
c739c21bb9eb938f5c15f4a67b212a04 *help/getProximalPromoter.html
f4fbcd3d28633d12d968a0f93bad13fe *help/getRegulators,Solver-method.html
f4fbcd3d28633d12d968a0f93bad13fe *help/getRegulators.html
cc12a378d405f66e1268ff3df68f787e *help/getRegulatoryChromosomalRegions,Trena-method.html
cc12a378d405f66e1268ff3df68f787e *help/getRegulatoryChromosomalRegions.html
ccafdb61144c41fcb1b8ccdd7a052bc7 *help/getRegulatoryRegions,HumanDHSFilter-method.html
ccafdb61144c41fcb1b8ccdd7a052bc7 *help/getRegulatoryRegions.html
caf55919f2468d48042ed60724276a94 *help/getRegulatoryTableColumnNames,Trena-method.html
caf55919f2468d48042ed60724276a94 *help/getRegulatoryTableColumnNames.html
a43dc5fe73144187a026d3392520044d *help/getSequence,MotifMatcher-method.html
a43dc5fe73144187a026d3392520044d *help/getSequence.html
310f54dfd58daca4f4b533b751446030 *help/getSolverNames,EnsembleSolver-method.html
310f54dfd58daca4f4b533b751446030 *help/getSolverNames.html
b959414ca8c93a73e8c17e4dd19d4120 *help/getTarget,Solver-method.html
b959414ca8c93a73e8c17e4dd19d4120 *help/getTarget.html
30919f4661d6e84b51b78d60f5bbfb23 *help/normalizeModel,PCAMax-method.html
30919f4661d6e84b51b78d60f5bbfb23 *help/normalizeModel.html
955d661049bdadafbb734a807b560454 *help/parseChromLocString.html
0660a1ae4957973a6b9068cb33d8c036 *help/parseDatabaseUri.html
7a32431fab6e80891ed3b67fc8fa7ec8 *help/paths.rds
52d20caf5c40882e35deca3ea4c80b28 *help/rescalePredictorWeights,Solver-method.html
52d20caf5c40882e35deca3ea4c80b28 *help/rescalePredictorWeights.html
d1365a6f57752f020651b9ad95575fcb *help/run,BayesSpikeSolver-method.html
c83e870eb945e7ee2a451023d6b17c21 *help/run,EnsembleSolver-method.html
0c598459b892bb243b99a04c93d467a4 *help/run,LassoPVSolver-method.html
9f7f4ac1752e42473f27ac88e2ddf954 *help/run,LassoSolver-method.html
a735f008da0d79d339737dc8c547629d *help/run,PearsonSolver-method.html
4ef3c41564240a2e2027a041046168ee *help/run,RandomForestSolver-method.html
3dc613688e56985fb8b4e34608e97762 *help/run,RidgeSolver-method.html
e2e89a7da301df6f85ddd679b8ded841 *help/run,SpearmanSolver-method.html
973d27e0061aca43cb6454d27515a0f4 *help/run,XGBoostSolver-method.html
d1365a6f57752f020651b9ad95575fcb *help/run.BayesSpikeSolver.html
c83e870eb945e7ee2a451023d6b17c21 *help/run.EnsembleSolver.html
0c598459b892bb243b99a04c93d467a4 *help/run.LassoPVSolver.html
9f7f4ac1752e42473f27ac88e2ddf954 *help/run.LassoSolver.html
a735f008da0d79d339737dc8c547629d *help/run.PearsonSolver.html
4ef3c41564240a2e2027a041046168ee *help/run.RandomForestSolver.html
3dc613688e56985fb8b4e34608e97762 *help/run.RidgeSolver.html
e2e89a7da301df6f85ddd679b8ded841 *help/run.SpearmanSolver.html
973d27e0061aca43cb6454d27515a0f4 *help/run.XGBoostSolver.html
49cc8e2626b46e6664579766b43b4c10 *help/run.html
65d2b059b26d3ecaccfca404446ded45 *help/show,BayesSpikeSolver-method.html
0453d6089ac0916c380e256e8bb21a50 *help/show,EnsembleSolver-method.html
c93366bcf70d3a001e4305146522d547 *help/show,HumanDHSFilter-method.html
31e07676897c5a20e8bab081de8c298f *help/show,LassoPVSolver-method.html
7296058740233325bb3d2f2913dbbe87 *help/show,LassoSolver-method.html
9f9ecb36c7dcf5b6ae62a995055dbb4b *help/show,MotifMatcher-method.html
35c1afae1c608a3e46331d2e3f6e4894 *help/show,PearsonSolver-method.html
ebf6412799e09adc0a036c660416749d *help/show,RandomForestSolver-method.html
a81a47255f54eeab1aefb0d3e7e1a5a4 *help/show,RidgeSolver-method.html
9822d7832356514481347e60c61e893e *help/show,SpearmanSolver-method.html
b8b1f3ee407a31fe9ee85c925074da1b *help/show,XGBoostSolver-method.html
c93366bcf70d3a001e4305146522d547 *help/show-HumanDHSFilter-method.html
c93366bcf70d3a001e4305146522d547 *help/show-HumanDHSFilter.html
65d2b059b26d3ecaccfca404446ded45 *help/show.BayesSpikeSolver.html
0453d6089ac0916c380e256e8bb21a50 *help/show.EnsembleSolver.html
31e07676897c5a20e8bab081de8c298f *help/show.LassoPVSolver.html
7296058740233325bb3d2f2913dbbe87 *help/show.LassoSolver.html
9f9ecb36c7dcf5b6ae62a995055dbb4b *help/show.MotifMatcher.html
35c1afae1c608a3e46331d2e3f6e4894 *help/show.PearsonSolver.html
ebf6412799e09adc0a036c660416749d *help/show.RandomForestSolver.html
a81a47255f54eeab1aefb0d3e7e1a5a4 *help/show.RidgeSolver.html
9822d7832356514481347e60c61e893e *help/show.SpearmanSolver.html
b8b1f3ee407a31fe9ee85c925074da1b *help/show.XGBoostSolver.html
d1365a6f57752f020651b9ad95575fcb *help/solve.BayesSpike.html
c83e870eb945e7ee2a451023d6b17c21 *help/solve.Ensemble.html
9f7f4ac1752e42473f27ac88e2ddf954 *help/solve.Lasso.html
0c598459b892bb243b99a04c93d467a4 *help/solve.LassoPV.html
a735f008da0d79d339737dc8c547629d *help/solve.Pearson.html
4ef3c41564240a2e2027a041046168ee *help/solve.RandomForest.html
3dc613688e56985fb8b4e34608e97762 *help/solve.Ridge.html
e2e89a7da301df6f85ddd679b8ded841 *help/solve.Spearman.html
973d27e0061aca43cb6454d27515a0f4 *help/solve.XGBoost.html
829394d0005fab868a8005336f0cbf77 *help/trena-package.html
6e1cea89f1c3ffc5a320b9cdc8c610b1 *help/trena.rdb
8255feffe3057e82bb6bedf2beee130e *help/trena.rdx
54c2d56e98afd29ba9e54c75e0f71d8c *html/00Index.html
4ff44ac2ede848858d5fc33e06ba6496 *html/BayesSpikeSolver-class.html
473ff22d77e8eafd23b4aecff4dd945e *html/BayesSpikeSolver.html
45b3aab1068b2a861e8e48e352a6865e *html/CandidateFilter-class.html
0e2ad32ec9eeb5c84aef21ecc6a482cf *html/EnsembleSolver-class.html
2d659594a77117f5d3a563ca4e75be09 *html/EnsembleSolver.html
0b4f4e2435aec6c011290c09e9658e68 *html/FootprintFilter-class.html
2be2180ecad5726331858e59fda14e2d *html/FootprintFinder-class.html
31a42ee798bba9dbaf47aad93c371631 *html/GeneOntologyFilter-class.html
0d38d27f77cf4d72fe5bda036c428971 *html/HumanDHSFilter-class.html
ea0c04c6cd7b70257bf0ca38973d57c7 *html/LassoPVSolver-class.html
4947186b640ee56ab521bea694f615b9 *html/LassoPVSolver.html
e9629c5d6b55fe4cbfd92867d1f9f306 *html/LassoSolver-class.html
d985d2ee4f406a3785b028cccbd444e4 *html/LassoSolver.html
5c10e3aaf94ddab2df9b036cbbb38586 *html/MotifMatcher-class.html
bc3e145c4c5da27a5c544fc0ecf49faf *html/PCAMax.html
ab831cc5a94878101a977fae54e148fc *html/PearsonSolver-class.html
d5cc63c01e9fe83cc0d1158769e51c3b *html/PearsonSolver.html
b6763e6916890c631fdc3f2643803b1a *html/R.css
afc45e4df92ccf53f5db3bd22b6a433c *html/RandomForestSolver-class.html
6fe25e845a6471dbce5e3446229ae997 *html/RandomForestSolver.html
46aa474bfb0c1c2baa10c0a9f60b4700 *html/RidgeSolver-class.html
7be089e5c5adebfcb47dc8620300406a *html/RidgeSolver.html
e6499945f2d8e531eecf9b1c8d339776 *html/Solver-class.html
65aa0bc9fb6fce37a84548bbb579e6d2 *html/SpearmanSolver-class.html
1116e9725292ded1a2c1461c4be17219 *html/SpearmanSolver.html
0cf3382c80dd354c3281dc74d2ffe597 *html/Trena-class.html
0944128159155056b75c5ff1f14301f0 *html/VarianceFilter-class.html
477f816c280669fad0e630031f347a49 *html/XGBoostSolver-class.html
90fdedbf6efcfe0623fbe751a2b9ba95 *html/XGBoostSolver.html
1b69390c076c9280b28c0677f15402dc *html/addStats.html
6412970c6f445abf2b58e2ac84965024 *html/addStatsSimple.html
1c16451053886865a34c4e13ebf1fcae *html/assessSnp.html
ac69b10f0f7586cd271b1f47e6d66939 *html/closeDatabaseConnections.html
caa7e0a923de8e07237d4dc15fd02a6f *html/createGeneModelFromRegulatoryRegions.html
ae7797b14e1cc5db553320c0952a9ab0 *html/createGeneModelFromTfList.html
3f03245b626ada57225ea1bde9f75252 *html/elasticNetSolver.html
204d7f94b99c1ebd0667e5537b842b87 *html/findMatchesByChromosomalRegion.html
288e7ef64662542486cc339f868c649b *html/getAssayData.html
1920568cd4ccfb936d6ee3dc5ebcb146 *html/getAvailableSolvers.html
2149993b6f89261b210750eebf8fcbee *html/getCandidates-FootprintFilter-method.html
c03526dfe1a8a04dd04c996151b541dd *html/getCandidates-GeneOntologyFilter-method.html
ba3c18be7d67a117de56767fab74e3f7 *html/getCandidates-HumanDHSFilter-method.html
3c1bd3e7c0e058b0b5305f2b8e6ba9dc *html/getCandidates-VarianceFilter-method.html
7e71e76eec54f6964007f04a60bc2342 *html/getCandidates.html
ea574e20663b1fae31c42b25902ddad1 *html/getChromLoc.html
9d62893e05b1bed61cb02efb464f5ed7 *html/getCoverage.html
e2105c50cad493566d92980a82f0a701 *html/getEncodeRegulatoryTableNames-HumanDHSFilter.html
be5c513e614085417de59c7814bd11aa *html/getFootprintsForGene.html
55c389ae28416407586a4b1d50dfcc00 *html/getFootprintsInRegion.html
8617f7d650ae67ae3a24cec7ad815667 *html/getGeneModelTableColumnNames.html
256c8b904d7b9b3bcd92d5f3417d4ece *html/getGenePromoterRegion.html
3189cc7e5617be29451ee909d289513d *html/getGtfGeneBioTypes.html
c76a4665bd975f1051097ac468edfcd1 *html/getGtfMoleculeTypes.html
0cabf6d36b101dc8142155d3788dc6ff *html/getPfms.html
a3dc9d494feab3c1c88521a96f7d8927 *html/getPromoterRegionsAllGenes.html
a9d1797c3a9e4d345ad0e7bb071f5a9c *html/getProximalPromoter.html
774f00113a5e0a0f376a99db0ae730af *html/getRegulators.html
17f57bca3ac8f2626e8fc1b615d5a591 *html/getRegulatoryChromosomalRegions.html
f481e60e86ad99c698cd4a4d0307f882 *html/getRegulatoryRegions.html
1f92265088a836284fac020ed435f204 *html/getRegulatoryTableColumnNames.html
8ef7b7210eca35730d7d70413636cdbc *html/getSequence.html
1413511c09422f77de41d9e253371a94 *html/getSolverNames.html
c6d120a7f3d454e0c98628721655e5ef *html/getTarget.html
5dc6f3baa1c8053230388b92de4d237a *html/normalizeModel.html
2da5fc072808a33d57de0219620d0247 *html/parseChromLocString.html
b3356802eaeb457749c4b9ab3018251f *html/parseDatabaseUri.html
33938f11c5dc68cbb35f60a93c8ca052 *html/rescalePredictorWeights.html
2592e57c32d6ac45b45a2f0924056ce0 *html/run.html
a1899caf7ceada568998e569941f93b9 *html/show-HumanDHSFilter-method.html
7d450acae14063cdba5575e6c1449cd6 *html/show.BayesSpikeSolver.html
69c1157708529570205d9d99d1b3a376 *html/show.EnsembleSolver.html
ad29b266d53da2a2e31bd7758136281a *html/show.LassoPVSolver.html
6bb87253887e05b25a167189766f180f *html/show.LassoSolver.html
a49dcf6117ef97b29c4f2c928bc26cf1 *html/show.MotifMatcher.html
c4150076323c5ae09300faad5de23c5c *html/show.PearsonSolver.html
ae87911e705bfeebdde5107372142daa *html/show.RandomForestSolver.html
849d53d4e55a6c13665cc0f6390b4009 *html/show.RidgeSolver.html
c70447dc4b6da34bf5ab6fd4621294ea *html/show.SpearmanSolver.html
4ef9501a2f430c6f9d70c2fd8ecd4021 *html/show.XGBoostSolver.html
5915f8956138b9c0d7c820de2eae9e03 *html/solve.BayesSpike.html
72d3b0826505344df6e043bfaca7399e *html/solve.Ensemble.html
c5f77dd1d0222899504aa1259d242c03 *html/solve.Lasso.html
d622122139ccc495c65a6005d1b154c2 *html/solve.LassoPV.html
fc793c6c45a7b541fa21ed15597bd61b *html/solve.Pearson.html
e836372ff852f29f1f66ef2c233f2771 *html/solve.RandomForest.html
53b1f5211361ad6fddc6a9bb698f2f9f *html/solve.Ridge.html
99f32852c3e2c5167ea2c46a21249aaa *html/solve.Spearman.html
ec39dac601b54fda62e08e3ee4dce5a1 *html/solve.XGBoost.html
5722891a0ab48edd7cc56393f0685e98 *html/trena-package.html
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
e285fc338974a9e176a79adcbc382612 *unitTests/test_BayesSpikeSolver.R
d7572d9d4166a897aebd7f11ded7eb52 *unitTests/test_CandidateFilter.R
b3c66e780ff247b8bbe6834feec6fa39 *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
bb1cc871b02e0df2a45a12204e7b00a4 *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
