e1145760aee37978166ce668cbbfe4df *DESCRIPTION
8f933a4bbf30de00052b90e1ef738f85 *NAMESPACE
a9ca4d69ccbd1cdc758f017cf62927e3 *R/AllClasses.R
333b160d4327d59bf1b97402324eb780 *R/AllGenerics.R
df6e0a766ba53880f27ba90d84e48bad *R/access-methods.R
25c635d9cf6c895b0e34cfc64e24e5c9 *R/annotationSpecificKernel.R
0fbf9ef1c6cca65f384dc7fdb44987d5 *R/coerce-methods.R
38c2e18f6b78736ce2c09e3022f221f1 *R/explicitRepresentation.R
aa8642c2a81aaa53f05459a29019189f *R/featureWeights.R
442280bd64219f9e966153e91d077b8d *R/gappyPair.R
1d40913d1149c6bb5507a545d595098c *R/gridSearch.R
3c203ac4b5775ea2f5742560d102e09e *R/heatmap-methods.R
646e983c454d4749e22f2dfc8767e9b8 *R/kbsvm-methods.R
809457d4f825827a24319c9cdb1743f4 *R/kebabs.R
d5fb105e12d22b00f1af1ff96425f217 *R/kebabsData.R
e2ebb6eeb9cfc5d253d25c9990b39fa5 *R/kebabsDemo.R
5dd157b75d371ab06b05fc9a8c6db7f3 *R/mismatch.R
974fd84d969d502f554fe5c79b55ac35 *R/modelSelection.R
fcc749b18fd8d2ab8d9592bdec872fd3 *R/motif.R
921444f21cf695ab3b573d8231cc7c8a *R/parameters.R
a6b33cdda0de2c722bfbccd0ff91fd44 *R/performCrossValidation-methods.R
84db0e38d33d2a9184661cb6e0e2410c *R/plot-methods.R
6309451e7c9a869cbc79d22e8f1ca54f *R/positionDependentKernel.R
cd3910595c18622418cb265dd9db685a *R/predict-methods.R
bdcacc4944581b9080df6775f62956ba *R/predictionProfile.R
5f3fce441025c92a023753d7b10f0546 *R/predictsvm-methods.R
3eb2b739b5efc9eef4805ff79b8db3f6 *R/runtimeMessage.R
ce6415ea972f4ae00f1c57354237b487 *R/sequenceKernel.R
b175bf056c58df620101c7ab95fe7423 *R/show-methods.R
947724eaa2f60cd5ad6e960049d6159e *R/spectrum.R
f6bf0839c843e6739acb7cf640a1c65b *R/svm.R
ba2d8e4f4fd794c1a1b683f19e64acda *R/svmModel.R
d10ce89ff31a02f0619404cda8830ed2 *R/symmetricPair.R
b3a7abcfc3943d4f6fca7279762e915d *R/trainsvm-methods.R
020f4a71e7068ead428af9e367159376 *R/utils.R
fa8869d8178fb5b4616a830bcb0ad470 *R/zzz.R
474ab8ea20328be28e0860e1b88a3752 *README.md
1bf18d9c216b8d95033f0bd2fe2906b2 *build/partial.rdb
f590886a33d8d0477909fcd9e00855df *build/vignette.rds
4b4f958c1a4bcb997d8b4c5384b9b6f2 *data/CCoil.RData
9abe439b9203868af8dd96500d68dc68 *data/TFBS.RData
2fbcbf933e28bcfb6a32c2dc5c7eca8f *data/datalist
a16e2a769af7afa19fcd852767e169e4 *inst/CITATION
c8bdca4f4e90023bb848d4761d48406d *inst/COPYRIGHT
95afac850fb8a57590e342b060004d40 *inst/NEWS
2f750525764b1fa6cf3cf6b5f9b7c151 *inst/doc/kebabs.R
8b8bd7b974235bb14fe91691a5e85aea *inst/doc/kebabs.Rnw
3ddbf478628cae6d43e99dfa7bb6ae0e *inst/doc/kebabs.pdf
57a92273743b8f6370160ca3f320c017 *inst/examples/UserDefinedSequenceKernel/SpectrumKernlabKernel/RunKernel.R
8e9a399995a435030ca948446c380f6f *inst/examples/UserDefinedSequenceKernel/SpectrumKernlabKernel/SpectrumKernlabKernel.R
2e680a1c80b396f0b4696d32d8ddb7ec *man/BioVector-class.Rd
f4be061869759de3065eb0333b8c977e *man/BioVector.Rd
ec3cd5057b38f4af74f46e560af44f4f *man/ControlInformation-class.Rd
a61d6b8f58320c10fc0a0771e26b5a8f *man/CrossValidationResult-class.Rd
12aabe6948840d5e7bb2358d3b20fee0 *man/CrossValidationResultAccessors.Rd
70e4d7f7f78d6917a4bc30ef0b9bee97 *man/ExplicitRepresentation-class.Rd
4a08777c62f689675443c4f8b1255d49 *man/ExplicitRepresentationAccessors.Rd
7f835607e6cc210b4f5ab635cf08b5b3 *man/GappyPairKernel-class.Rd
e8bcb1cb532a13cd4d0231b6a0e1e9b3 *man/KBModel-class.Rd
c329b51a36edc961e538a379abfcae65 *man/KBModelAccessors.Rd
a0e493d00db450c02d3946a319405f52 *man/KernelMatrix-class.Rd
4d6438e81052aecdcc8d2f666ef0dbf4 *man/KernelMatrixAccessors.Rd
31c1fbb9759138be9ea4971eb1f2f568 *man/LinearKernel.Rd
4fd19425ca0929a046ec4fecbe5728f9 *man/MismatchKernel-class.Rd
703c682750b07e0652c6e4069a69143a *man/ModelSelectionResult-class.Rd
474cecb78170afa1ab45da861213a2b5 *man/ModelSelectionResultAccessors.Rd
de2b740c2ebad5bcb61ba2561661f5a4 *man/MotifKernel-class.Rd
e8e74a8613c948fdfa452225676ba02a *man/PredictionProfile-class.Rd
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d5ee0e7daf9a091a1e42ae5c1793b78d *man/ROCData-class.Rd
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f027e1bfcf10be09b88ca11baf18ceb8 *man/SVMAccess.Rd
fb3b2b58f0b311b15c98aec8c2158b81 *man/SVMInformation-class.Rd
067ec22241a5bd7b69c008fdde3e10f9 *man/SequenceKernel-class.Rd
6117bece56749a4705c9969abec24fa0 *man/SpectrumKernel-class.Rd
daaf286e22d87259b4a4008aa59b4cc2 *man/SymmetricPairKernel-class.Rd
42c17515ed5c2702ebc368dd2236004c *man/annotationSpecificKernel.Rd
0d3b4b11ccf58d1442df2405a9260f63 *man/computeROCandAUC.Rd
19de88962974fd6f3475d87fcdd14121 *man/evaluatePrediction.Rd
3dcbe7eff831474f784c3ffda0829806 *man/explicitRepresentation.Rd
4dbac426161b0ff80fff4c3d70bda5ac *man/featureWeights.Rd
9bcc787cbaf11ecdedcee0c144e06709 *man/gappyPairKernel.Rd
a1ecebdb9731fc853a3f2ce5245417fb *man/genRandBioSeqs.Rd
7544a132ce50484daf87ab6c831d62d2 *man/getPredProfMixture-methods.Rd
4844e8f29e74b1a4b4d9df61063d7809 *man/getPredictionProfile-methods.Rd
4967ea80576faadc62c8f97933fa7351 *man/heatmap-methods.Rd
6885a2054bb6d8bfae56234b66bcc1fe *man/kbsvm-methods.Rd
caef3010e189d272c78b5c429c04fb72 *man/kebabsCollectInfo.Rd
909eb8ec622d9cd8e9254b70ea745477 *man/kebabsData.Rd
65c5ea9c394b7ea5f761f0f420afc217 *man/kebabsOverview.Rd
d1b8a110ff2cca26acf061920b8f3f7a *man/mismatchKernel.Rd
07175e7237ee87d2cc0879d002ead2d4 *man/motifKernel.Rd
7049bd64e8c5b09be06019c4f95ecbbe *man/performCrossValidation-methods.Rd
1f56eceda223e36f0bcd91718b3e7695 *man/performGridSearch.Rd
353566079820b73a3d08152529c98419 *man/performModelSelection.Rd
3e8cea70e48f49ed49dd508e832b2236 *man/plot-methods.Rd
9f69bf044242b7a158c95cdf96ccac22 *man/positionDependentKernel.Rd
211ba774dd9e3dfaa4bbbf1c04d58fcb *man/predict-methods.Rd
cc853459bac5f30c677f0c7b56d51de8 *man/sequenceKernel.Rd
10ec7d1bb77817ccf1c2be2338263622 *man/show-methods.Rd
4119ef2c6a200c4474fe83f43e6618fa *man/spectrumKernel.Rd
530ba0a5ecf4263be3748f2bd4864651 *man/symmetricPairKernel.Rd
f1f4685a8f0afb74e19c344a86d86b22 *src/Biostrings_stubs.c
eca6600f7e42be93c743984800f3efd5 *src/BitArray.h
f1a403f18b329bd061a0935f91fb504c *src/ByteStringVector.c
98d3f0d7f96f449cd11d5cb5314d9068 *src/ByteStringVector.h
63c3bbab4d95beea377878bc09207242 *src/ExplicitRepC.cpp
5a206cf81f80bb5ef8593b0109f2f2a9 *src/ExplicitRepC.h
7e2656ecece6d436f9bbd3c44a2f0f13 *src/FeatureVectorC.h
dd415ac533b0030dd5b4191f4ef72418 *src/FeatureWeightsPosDepC.cpp
a668a39dae3a1eda385054a95ff3c142 *src/FeatureWeightsPosDepC.h
2f68f1856db5d44f099c6c737084a927 *src/GappyPairC.cpp
dd2738665534350b695c4f6989121538 *src/GappyPairC.h
b0447144238dce005a1fa8a625d1563c *src/IRanges_stubs.c
5adeb2b3bf361053555070f8f09de25f *src/IntegerPowers64.h
2796d0c68442170d5f1dc68130dab3c7 *src/Kebabs.h
473851ab663579be4ccffa266fa61361 *src/KernelUtils.cpp
6536d6527f5725410af10501108211e3 *src/KernelUtils.h
a4a70b51bbf10233f95aa5c827c28872 *src/Makevars
a4a70b51bbf10233f95aa5c827c28872 *src/Makevars.win
22ae8f9701a7c317fc8b8594c8023b70 *src/MismatchC.cpp
52525ca45136b4981c1400a7e17affa9 *src/MismatchC.h
7fc4480061747d9f5fa35fc7e13a320d *src/MotifC.cpp
c6b7e94ea0dcc45882b4435573dbc27c *src/MotifC.h
012fc38bc740afc1382670e13ecb6dd7 *src/PredictionC.cpp
c76cbfb0cb0854e067b3637011dcb968 *src/PredictionC.h
8bd33d82f38b52197f1e1ef24748484b *src/PredictionProfileC.cpp
0e3be572cc5d5716c2c47bff78b55123 *src/PredictionProfileC.h
59a6b833f89ecc9aafeef863cb663afe *src/R_init_kebabs.cpp
9b13f0eb4cd7d92bad98546c1cebd8a4 *src/Rsvm.c
2cbd9616c9bf1588ea20009e14e8ccba *src/SparseMatrixHash.cpp
68c2590ec8d69084301eddbfb8de380e *src/SparseMatrixHash.h
2df5905c58e9947b06da9bdb18e068c1 *src/SpectrumC.cpp
9e0187efa2a9bc36ae42a07890cb7ca1 *src/SpectrumC.h
341c94f0ffe185314f512d05659e8e8d *src/SymmetricPairC.cpp
76cf01004d1996d00c6a0b9e0589d5bc *src/SymmetricPairC.h
5cf35797cecd92caa206422d5d64c0a2 *src/Utils.cpp
57c7bfa8aefb9f830a0c29c8dd1841ba *src/Utils.h
07fbf9ef7d1a296302e6de26aa821a44 *src/XVector_stubs.c
437db55a15451fba4e9419de87377c61 *src/khash.h
feab3c1929bf7bde2a70ecba8b000856 *src/ksort.h
9c29f5eea843e7058812045a96204564 *src/svm.cpp
7b8490615f65297cc224d32436faf650 *src/svm.h
4d0f2119425bccd76c4cb7b74782bd06 *vignettes/Heatmap.png
8b8bd7b974235bb14fe91691a5e85aea *vignettes/kebabs.Rnw
00cd717d07e0e2b3902667116aa98d75 *vignettes/literature.bib
1c8843383c0bd05870c45fa0ebea6cc2 *vignettes/natbib.sty
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0a5a7cb02ced0783bc644e601b48c8f6 *vignettes/ubmanual.cls
