f66abcbe5ad54551cb11da6a1a9b0edb *ChangeLog
f83cc1c38fbec45e6e92c3b84b029252 *DESCRIPTION
9f1adde363c932188401eec040b5f30e *NAMESPACE
43f15bc4aafd28cfe7d481d590d733fb *R/CNORbool.R
d833571f9bb8c8b75968a6ebf4642280 *R/CNORwrap.R
0d3966d4c7e96477fd1551ebe9a2b7d0 *R/CNOdata.R
ff7cf05e72cf29a76fd1b91cfcb7017e *R/CNOlist.R
a31268d5758ff261b7723f9475859b00 *R/CNOlistDREAM.R
bbfbff54245ccbafa6857012b27d2acf *R/CNOlist_ToyPB.R
e0edf6568e852b302ed18d8e2df859aa *R/CNOlist_ToyPB2.R
df5ef58539d1e9f8313a951dd03b4803 *R/CellNOptR-internal.R
bb4aef564a942e5e95b0b325f34d31a3 *R/DreamModel.R
5227374da7ce20fe8763e5a74e0e2e36 *R/PKN_ToyPB.R
1ed05db89e6cc07fbea726da4f41bd83 *R/buildBitString.R
f81f42fbd2633e844bf440c867c9234c *R/cSimulator.R
2e649b25dfa9d7f5ec38c100f4ac7333 *R/checkSignals.R
dd97aaebab3d54ad1e0c0297579d2a6e *R/cleanupILP.R
74da0b043975cfc4145c26f8288b839a *R/compressModel.R
4de642fc58f9fce7ee556074bf99607a *R/computeScoreT1.R
4216d821cba828ddcec81864a73838c8 *R/computeScoreTN.R
62e8ff745d7b7d9bb4a03326c99ab19b *R/createAndRunILP.R
fb1c7b904fbf01f95734c4da3a4ec116 *R/createILPBitstringAll.R
3399b16f7e4e3553cc916e9db9f49294 *R/create_binaries.R
b8f47609345cf8d4ceca3a283a2c604b *R/create_binary_variables_for_all_reactions_z_i_in_experiment_k_i.R
ff44190b8199104c021e7a5cea13ca67 *R/create_binary_variables_for_all_species_in_experiment_k_i.R
3e724902bc20cb75d6efbee40d0590f5 *R/create_binary_variables_for_y_vector.R
6ad5b237bd807696ede355a5cbd67711 *R/crossInhibitedData.R
e17d84c0d43b76ee7c21a83d7f58838d *R/crossvalidateBoolean.R
cb6718bb289c5a667ad51edf8cb6bb32 *R/cutAndPlot.R
495ad31629466cb952389bb53aaadbc8 *R/cutAndPlotResultsT1.R
31819f21de8377e77bab5a9490611386 *R/cutAndPlotResultsTN.R
1d8dcfe4522b748bae9cfb963675e9a1 *R/cutCNOlist.R
a3791773679e7cd261c47033d301a40c *R/cutModel.R
303d982d11819309f81432a30abda6bd *R/cutNONC.R
49e60ef98122a4a84e83557a4820b8d6 *R/cutSimList.R
384c448520b30d2dfcee48b636118cf5 *R/defaultParameters.R
80c55e1a9c9ba4abc7fd058b36d4d9b7 *R/deprecated.R
79a7753d3211cc4796cf05bea700ea7e *R/exhaustive.R
30bca71190f01459d604526d33ea17fb *R/expandGates.R
10fe7d0366c089ee2d888c53866ad2fb *R/findNONC.R
55793b4fd7c3c9fec57d8d460714b630 *R/gaBinaryT1.R
8f94dde1bebdde9ca941bf0427e7da97 *R/gaBinaryTN.R
8ecd8b1a431a5fc2ea4dad6866369e2c *R/getFit.R
096fe5a2c8caf28dc1f2a104662fcc34 *R/graph2sif.R
e04b19f8ffb2921c11d0783074c6300c *R/ilpBinaryT1.R
d2a3468039494b5ea86722005b166b06 *R/ilpBinaryT2.R
cc24c296c5a9e29b0291ce5d103c09b5 *R/ilpBinaryTN.R
4e42ea798836cf1cfb79b3655dcb6fec *R/indexFinder.R
283d31ebe0b0fc747017f03d4ab3727d *R/invokeCPLEX.R
344d3505b5728b8c362e9eef1b003101 *R/link_midas_colnames_to_namesSpecies.R
56a4243e94a7f3f4ce7378244fae52f4 *R/makeCNOlist.R
a86900437b2427aa5eecf8537bab2959 *R/mapBack.R
c00d5531288734adcbc2e485f29cacbb *R/model2igraph.R
c42be803018ab9ee42bb3e44ec6b28be *R/model2sif.R
22c980198a233d79515a5c842b8a85ce *R/normaliseCNOlist.R
2c6ae69f5a5a7890efaf975324ff129e *R/plotCNOlist.R
020ee5c389d944eec6eff9eafb14fe54 *R/plotCNOlist2.R
6df85e8bceb9dda576495bfccc72b134 *R/plotCNOlistLarge.R
bbc57c69f815b733100139a403702cff *R/plotCNOlistLargePDF.R
7c479a1ee93d9f31a4c2dfa04740e52f *R/plotCNOlistPDF.R
7d35352da156ba33bd41ecad5dd321c1 *R/plotFit.R
f12f155283dc10e9fd59452c2783f4b0 *R/plotModel.R
44c6304519598c430bd54f93917584b6 *R/plotOptimResults.R
acdc61f44c9b00cbfe0dc954995f1918 *R/plotOptimResultsPDF.R
79b561eacf9a0068b6a0cf31be7c3fd0 *R/plotOptimResultsPan.R
df0836ef0efe0d6b4e643e02086c6ef3 *R/prep4sim.R
66fe829f0a8928dc9aa07ccadb6145b0 *R/preprocessing.R
cc1a55976d00ce5eba657d1d167cc09e *R/rSimulatorT1.R
18a3d048ad60fffe7e66e73072134dfb *R/randomizeCNOlist.R
85399d7543b436dbb41ad0a865721735 *R/readMIDAS.R
23c026b75a354ea7acce2479587cf83a *R/readRules.R
8388979d6dea0fe00e45b5055e8c2a9d *R/readSBMLQual.R
b4430b088c0c81f5530dca3bf8aebe02 *R/readSIF.R
9f4c5f7fdf5ce8082bc1bb1e4ae59556 *R/residualError.R
54c009a30425e050b00633c663a16d54 *R/sif2graph.R
53f7fbae40bc79d6e2d50f5a3907f706 *R/simulateTN.R
94caf73d2943f5c21564c4fad36b175e *R/simulatorT0.R
e253b51022195fa5675202f50f50f8c3 *R/simulatorT1.R
85667e568f58c9d9f10a1e7130f98be4 *R/simulatorT2.R
aa8e4427075c0704c89825338115a6c5 *R/simulatorTN.R
115900d2032c06fdbe850f26bd4bdfaf *R/toSBML.R
e1fb29bbf0bf9f1d75ce1cb660ddde0c *R/toSBMLStandard.R
7b257c9c6aad35ab48489c0de0f95e90 *R/writeBoundsForEdges_y_i.R
8269bac6ae2a0f4074c445b8e5809a8c *R/writeConstraint3.R
28e12126740b1a875a9cea859580d356 *R/writeCplexCommandFile.R
a8dfd733e2807b59960489681d9a2fd0 *R/writeDot.R
550c4aba5d76737d83c4b2144ad21086 *R/writeFile.R
9fb81dcfb6363280abeb92cadcf6ec7e *R/writeMIDAS.R
6beb9be47fcec4e16f94d1c1eb332ec7 *R/writeNetwork.R
34e8d1084297cc8fd8835e29706bcf5d *R/writeObjectiveFunction.R
ad4d8a41bee7b1036de001b570c0a215 *R/writeReport.R
195e9f9edab983d9fd7ae926c150e33d *R/writeSIF.R
dafabdca544ab45f28d4742837ee0d9a *R/writeScaffold.R
cfe06e9e865b572403aa46596a04b275 *R/write_bounds.R
5183c1d4eb40aaf1e4745b0067455125 *R/write_constraints.R
a7becad743b7c60e84a117ca8def793e *build/vignette.rds
88146a03084c295a87a7447dfd43ca0b *data/CNOlistDREAM.RData
ee79d293ac9f2ee22b9bbffe6f5c7f96 *data/CNOlistToy.RData
0e858bae27cc5f60e97e9a883749b1ae *data/CNOlistToy2.RData
72547f5ca1fc648f43e31ecb41545d63 *data/CNOlistToyMMB.RData
a3ad2774d4f61055c332ddb55bc303be *data/CNOlist_ToyPB.RData
035f1dce48785c25e98e1b1dd23c1aeb *data/DreamModel.RData
064736c560edafe75644f713412de9b4 *data/PKN_ToyPB.RData
0426b6de1a9281228ed34284aa183231 *data/ToyModel.RData
d623b3af66f90e0dada5b21ecce59047 *data/ToyModel2.RData
7a8f92357548f685794b373fc03cc7b1 *inst/CITATION
a5ef772e3b4f13e5b2d0fe5450139757 *inst/DREAMmodel/LiverDataDREAMMIDAS.csv
7fe98547d5c6107fb8f93d96dd665d8f *inst/DREAMmodel/LiverPKNDREAM.sif
e6ce326933b77287fc310d58b56fdc8a *inst/NEWS.Rd
d6e7e2bd73f1380af73adfd390decbb9 *inst/ToyModel/ToyDataMMB.csv
1ca78d17dae87816e1d8eac9455f182e *inst/ToyModel/ToyModelMMB2.sif
fb6b7fc0528633ddb5f1f9d56deb49a0 *inst/ToyModel/ToyPKNMMB.sif
ff9ab2aeb0659a70e1f92185e337055e *inst/ToyModelT3/ToyDataT3.csv
d6bd3e368322dacec8f9a4ff044d8cb0 *inst/ToyModelT3/ToyModelT3.sif
2a3a04c10fb80816b9fea5abd65a7743 *inst/doc/CellNOptR-vignette.R
1f9de889af2e3177508c4b401d925e19 *inst/doc/CellNOptR-vignette.Rmd
386ace730a1c050324060bfe7a1f0f30 *inst/doc/CellNOptR-vignette.html
8706931af67c6959381bf96b7b75c017 *inst/templates/CNOR.css
b1f9e0c4c3d71777139903bafdbbafec *inst/templates/Rlogo.png
39ce3fe5657454ce228c21690640de07 *inst/templates/bordercorner.jpg
d825ab722bc1cb5b366a49c06cc9bfd1 *inst/templates/bordercorner2.jpg
ea48ed430bd9af8025c74612c9b4d477 *inst/templates/logo_saezrodriguez_mid.gif
b92d74ce744aeb6f72c7996692dee627 *inst/templates/phinou.jpeg
aa6cb4f9790d56975496ab88b0434a26 *man/CNORbool.Rd
09f2319352b66172b088790aee78f34b *man/CNORwrap.Rd
7ccaf09c988297a537a7affd159504ec *man/CNOdata.Rd
a76f4c767d83f9f0e124eb0b24b3cd97 *man/CNOlist-class.Rd
4b5d40557b2b450964a410c1cc6ce9d6 *man/CNOlist-methods.Rd
2fbcee190a67226520e4f26ffbfce34f *man/CNOlistDREAM.Rd
b2d5657d9c4b80e410e27ca65975c3dd *man/CNOlistToy.Rd
8d077d9fdfca8cdc99a7377f75ac2046 *man/CNOlistToy2.Rd
b2f7e6c5d0ee0b60213ed4b6e9cffed6 *man/CNOlistToyMMB.Rd
71cb80b99b856d54e7ca1e14e2f441bb *man/CellNOptR-package.Rd
fe774f6e517e6764a2bd9e6e113b8d93 *man/DreamModel.Rd
853d6451b21ac2ae8f385a1e5e82a519 *man/ToyModel.Rd
e19b49949d71f41b309229f4abe4c23c *man/ToyModel2.Rd
dea7a3cffb532109d5e0cb56d48e712d *man/buildBitString.Rd
aad5e17f36a96876c6135a1f7423e931 *man/build_sif_table_from_rule.Rd
d3da7801e96452750f2bdb169d656055 *man/cSimulator.Rd
313323b5a7bb17e90f491d06a5797677 *man/checkSignals.Rd
7122e729eaf44da2e1503151d5d26306 *man/compressModel.Rd
c3983bbff747b61794fc30b61b34b200 *man/computeScoreT1.Rd
0a3f7d6e09f9df9e41e5b09daf4094ec *man/computeScoreTN.Rd
2ce279f837d1a7d11dd9d576e57ca773 *man/createAndRunILP.Rd
b12a9dff3c63ba034d45d87b88bb9f07 *man/createILPBitstringAll.Rd
05dcf88018bdc7166daba51ec73ba31d *man/create_binaries.Rd
0f1daa7ab25df6ac6acf223964eac24a *man/crossInhibitedData.Rd
b93219578956d13cbe1ab59c074ebfef *man/crossvalidateBoolean.Rd
39ed0e9370c73a2d0eafda40f261cb97 *man/cutAndPlot.Rd
fe00c7af35a4388e62766aded357c9a6 *man/cutAndPlotResultsT1.Rd
909542187474f71fddca3a836fd078aa *man/cutAndPlotResultsTN.Rd
2d5a5118c69d47679d6f887e844b6aca *man/cutCNOlist.Rd
0a002c5db06dafdf941d455a468fd2fb *man/cutModel.Rd
ec9a531264ee33fa2bf427153f9b11ba *man/cutNONC.Rd
cfc8675f1a7e244a103c1a80c8d7f36f *man/cutSimList.Rd
cc2c322a11c7b1eea700e334be35a258 *man/defaultParameters.Rd
1a57d99ac99e86371258290caa8a9a28 *man/exhaustive.Rd
4920449275efaf5b3662d3b5a5ff0f59 *man/expandGates.Rd
f337dad7c49a3810bca946da362c4f28 *man/findNONC.Rd
0808efefbfacbd92b5cacffcf9b9cec5 *man/gaBinaryT1.Rd
cb05b9d466828c28143289384fab513b *man/gaBinaryTN.Rd
98d9f0b167d8e66726c3c49b130fddd1 *man/getFit.Rd
e9864f4d803ce9b6d91b631a39f91a38 *man/graph2sif.Rd
1b26b12927a537bea40cee3d7927f3fa *man/ilpBinaryT1.Rd
88628f44e659452210a5566e5f54fa2b *man/ilpBinaryT2.Rd
7488d3aae062772d233790d399c6e26a *man/ilpBinaryTN.Rd
4fc1c62f8207979ec7b5d81398d7e09a *man/indexFinder.Rd
0446c3cbbb3468b0fc193bcf006439c5 *man/internals.Rd
4a0f108faab6632a6433e126d649a306 *man/invokeCPLEX.Rd
b14a34bbe906021e7749a4e43f82f3e9 *man/makeCNOlist.Rd
418bac57422beabd5d807a3b755f89ef *man/mapBack.Rd
f20e04794adade775570c28bd3602641 *man/model2igraph.Rd
aa34591635776f6caf6a8719206b2dd2 *man/model2sif.Rd
c45556805952bc4ef6972e0223c6e24c *man/normaliseCNOlist.Rd
57c9c32f57e1a5f1fb91ad8a6d2e3e1e *man/pknmodel.Rd
0c61f96fcbb9c33fb0722af08e5cc25e *man/plot-methods.Rd
d6e76291948d79a3982ad9af413da768 *man/plotCNOlist.Rd
a0aa46c72b4a44062c79f00717485a58 *man/plotCNOlist2.Rd
9e19c8fb0c47f3f910b69011ce1bbd00 *man/plotCNOlistLarge.Rd
2149d702c7c09de78f440ae4425ea62e *man/plotCNOlistLargePDF.Rd
a566de4c11aafda0769aa87c2654e702 *man/plotCNOlistPDF.Rd
ecb081bba6dd94323a875c9d1c4518a7 *man/plotFit.Rd
c355f01fac232499628ef8eef0c0af2a *man/plotModel.Rd
a06b32a41861f6fccb4c413acf5bcf6c *man/plotOptimResults.Rd
f6f41663da5154296637d46cd182779d *man/plotOptimResultsPDF.Rd
0deb66d97a8723161c751166c75464cb *man/plotOptimResultsPan.Rd
837ca8184d4d76812aad9f469b4af103 *man/prep4sim.Rd
82a9f9f50835af7094b3ac16f670c6d9 *man/preprocessing.Rd
10611b17fcdf8ff3354a9313beb69223 *man/randomizeCNOlist.Rd
cb61c908d1798c68cb131cd92ab20de6 *man/readBND.Rd
38662ca4e45768beca573587a8501a59 *man/readBNET.Rd
36b2490cfa7013b8d1799ee5c6f9ad47 *man/readMIDAS.Rd
ab8bee5023b68aa96a0fe4d3b126d5c3 *man/readSBMLQual.Rd
5e46e258ced20dda99f9c05165706ad1 *man/readSIF.Rd
dc742bc9e563cd59f572fe552a71f5eb *man/residualError.Rd
fc31ac6f0e471cb612a384cbd876eb9a *man/sif2graph.Rd
31cad8d0594d6d9f836be8f49f242905 *man/simulateT1.Rd
da3519373b5911dfa2bc71ce4426b8c3 *man/simulateTN.Rd
f531ae56b682b7c21c0377a6b22ecb8d *man/simulatorT0.Rd
c382ec19ac42cfc792b8f13eff53e1d0 *man/simulatorT1.Rd
db4843c81186e3b98523096f5fe13315 *man/simulatorT2.Rd
17b121ed5326ed36540652848b8a82da *man/simulatorTN.Rd
a8436f3fc6fb3401a6d28fd0844a79ac *man/toSBML.Rd
8bb783aa1590624cd163a82309a75a3a *man/writeDot.Rd
da587a91764d6abea89a5ae91b10e6c1 *man/writeFile.Rd
1bc127c17d092d1db265b45c4b98afa7 *man/writeMIDAS.Rd
c1382d471f5caaa2dd19ba2850974327 *man/writeNetwork.Rd
e39767565046bb335ebcc927987202b4 *man/writeObjectiveFunction.Rd
1b109bb9eab5291a5e55afd3d741fb62 *man/writeReport.Rd
88f56250b677689aeb31d826fee03c64 *man/writeSIF.Rd
1d5165dc6bfedcee21ef95dbfbbb337b *man/writeScaffold.Rd
4be73007882bc1bbd66dd946e8752fe6 *man/write_bounds.Rd
db63bca0b42fd6287f2b6a296d4f7862 *man/write_constraints.Rd
4c0421f2b5881a3eaaf0e13ca4992d00 *src/Makevars
a3b38eb8b99e9bc7b4a12d61d2b67df0 *src/simulatorT1.c
edeae2756519d19ce9afbda6fd2eccf8 *src/simulatorTN.c
64e1af0a585f8888a413cec127c5ade6 *tests/data/example.bnd
bbaf16d27807a00e507fa45f8291a4bb *tests/test_gaBinaryT1.R
184ece288221ed0eef88de29d63d4c0f *tests/test_gaBinaryT2.R
8e726e01030b1cd57f9f1eba4a449b0b *tests/test_gaBinaryT3.R
d31ae375cc40c078a452472c1ac031fc *tests/test_import_rules.R
99b37a6f215d37e2fcdd0f031620eeca *tests/test_manySteadyStates.R
ba156c2b4d5bb1120d62de582a55df84 *tests/test_priorBitString.R
23005a8f12b5ac7fe23c589be48d6cad *tests/test_simulateTN.R
1f9de889af2e3177508c4b401d925e19 *vignettes/CellNOptR-vignette.Rmd
654be87a01bfd9ead39d44869e742dbd *vignettes/CellNOptR0_1flowchart.pdf
29ae5dc5fbef97b6c180dc091fdce385 *vignettes/Fig1.png
4f1c0f3da539df563b8d056b557ed05e *vignettes/Fig2.png
1b2170d073bb8a2976b8746c6e4f31d3 *vignettes/Fig3.png
43bcf957804343711e2d7030749c6759 *vignettes/Fig4.png
5be95e24a8eabe466760162af0ced4ed *vignettes/Fig5.png
5ebc5d3c1d9b315cb6b871f2aaca78ae *vignettes/Fig6.png
3cfa23a6b7b6d6286b64ada516d2fd2e *vignettes/Fig7.png
4bac058a3727142bb1aa8716be272b07 *vignettes/ilp_fit.png
92498c241ff90823756b2c24252ad2cc *vignettes/model_1.png
022cbe03113fe462b8e0fb493f487f69 *vignettes/model_2.png
43ba03ef1609ade70525f94f7bb4aa1b *vignettes/model_3.png
