37a69acd1a63005ed48a6b0755a23be6 *DESCRIPTION
9307b8b1f3814b4a53ba318967ead29e *NAMESPACE
65daba038aa56b8a2eb7fbf8a5a10766 *R/Coordinate.R
f9c3e132b61b20f86e8d59df025bb2aa *R/EXPLORE.R
55057aee43bb25cbade494c6ab6c5735 *R/Kmer_Table.R
88f57b1386afe2a7a52b4071a72c5446 *R/NCBI_Genome.R
ccaf63dc7b5cfac0bfc27a349c7a0339 *R/RcppExports.R
4bce295d2797e30e60956db8266d9d64 *R/SCORE.R
20ac4c3936d69c78ea39cbc3c9392ba1 *R/STUDY_ACROSS_POPULATIONS.R
3276516e13081f87588ba3c57f2a57b6 *R/STUDY_ACROSS_SPECIES.R
fbd1821e7246ad1f32322aa5140b401c *R/STUDY_CANCER_GENES.R
3e193dfeb4a7a87c0c7613531ee5061c *R/STUDY_GENIC_ELEMENTS.R
77a311534088d9d54638550f5b595177 *R/UCSC_Genome.R
d9569000bae2194d0795f8390f9e79f7 *R/addAlphaCol.R
633a353f01ab9c795777486013ed264a *R/bedToCoor.R
d4fd29a4df5d08e2a3b291194b952cc1 *R/buildControl.R
c1879f84269f0b927bdff12a8f9fbaf0 *R/buildKmerTable.R
0c6749e8d7a272ce7913254ef1b820b1 *R/buildMidPatternKmerTable.R
7a2e93dbe20a27a293d033786a05c05d *R/buildRESTurl.R
3d7ccae4be3f3d7f7ae5b886195b29af *R/buildRangedKmerTable.R
8589a6c743c9f4943cb36420ad78b299 *R/calKmerSkew.R
54fc8ce3c304ff62f3e5076abeb7aab6 *R/calPWM.R
ce9c29285e65c976a086bb3d2c5e5155 *R/catHeader.R
4a7dac8d5b8d6deb39fe818b27e005fe *R/countBaseComposition.R
da88a80edb627d2086a0840993d48f9a *R/countChoppedKmers.R
7da4da29ded4793f8790c89c6ba3b83e *R/countDistribution.R
53eed31e537b029cd0f0d8cf9babaa26 *R/countRevCompKmers.R
73dd50bc958d693bc4b03201d3984582 *R/downloadNCBIGenomes.R
09e7e57152345537527fff4b10bde58a *R/downloadUCSCgenome.R
624ef17d65b327d51d719989a372fe90 *R/example_genome_coor.R
a8b00a499836f276627e1a302aea0861 *R/example_kmertone_score.R
7d0008c1aaa3d704aad57b76d87c9b61 *R/extractKmers.R
bfec8afbed3e92adbc32318a8b8a8272 *R/generateGenicElementCoor.R
7b7ad4e85696da5c0ee911b20adaf435 *R/generateIntergenicCoor.R
4e3625fe09ae843b1392c380cfc6b18f *R/getCOSMICauthURL.R
f32289b0f057746b676069fd4ac65d5a *R/getCOSMICcancerGeneCensus.R
5a3bf2047ca8b810c848f210951a0a30 *R/getCOSMIClatestVersion.R
f492eab867d1da68a57b16fcdb71325e *R/getCOSMICmutantExport.R
3aa1f18d2374738dc57fba4dc5e56527 *R/getEnsemblData.R
5badd05f118d3240bd473887d4e3e6b9 *R/getEnsemblRegionFeatures.R
c28048a5484aa445feb2bf79ea104080 *R/getEnsemblVariantFeatures.R
9d4626dc6393baaaf4a439bd8fa75ef0 *R/getEnsemblVariantFeatures_serial.R
bbf74415efcc7af728cb3323e19264c4 *R/getGnomADvariants.R
e683f3a1458b9c8e3ecf8fcf2a23354c *R/getICTVvirusMetadataResource.R
e9b97585d9dd5ef1835619ec97443ab4 *R/getNCBIassemblySummary.R
c6067806edc4ea5e6f81f511ff8e98b1 *R/getScores.R
28c1f9af9812eddc92411bf0d2919318 *R/getUCSCgenePredTable.R
3f5f451392fe3a483796a68ae58a5859 *R/getVCFmetainfo.R
778c4fbea840b1246ea82cfd25e360aa *R/initKmerTable.R
270e0efab8c7b4b0d26fd8fe4f178cfa *R/kmeRtone.R
d8958c54d3558a4dbb995efc78135071 *R/loadCoordinate.R
d57e50a7397c2195fe0173299ff57f17 *R/loadGenome.R
c4bf6bc56b3775a92c7f35eb6631e94c *R/mapKmers.R
8df6e0996b50ef94d2046d0b0df9cb0b *R/mergeCoordinate.R
36f71aee7598c6b88e52b75e15f928a3 *R/mixColors.R
c20fd34676bb5a8fe86317629b0931a2 *R/partitionCoordinate.R
57133a159710e843e94ec856107c5832 *R/persistentDownload.R
a879ad4f91a317edf151e8d90b23f2f2 *R/pkg_attach.R
ff732086f6c5330559cf65cb3e7e56d7 *R/precomputeGenomicContents.R
da8cfd18cbc5a5bc0def9b7979fceb7e *R/readBED.R
54485a5cdcdcf14ae1c6a1be64d58eb7 *R/readFASTA.R
a09db7b88224eb1d7e4422cc92ac0632 *R/readVCF.R
a29798401364a5e0a9fafb729b9133b1 *R/readVCF2.R
3cb8030ad6c9ccd99e6fb678664b2171 *R/removeRegion.R
b86ad4366375b5dd16757ffe9db389df *R/reverseComplement.R
da5a93a89ff560e7173aede22ee44393 *R/scoreKmers.R
40a0c28c78fe96e842f5b2a684eac1f9 *R/selectGenomesForCrossSpeciesStudy.R
acf01f2bd2648dd545ac58a87db1cf8d *R/selectRepresentativeFromASM.R
2ff021e96b75eeb2bd314a0c1d0a4148 *R/splitFASTA.R
435fd9f878cffea1846549816c929ff4 *R/system3.R
350ecf79f18cb304d1e7a3a9adeabdec *R/trimCoordinate.R
b0860ae7930b190e649c9303f3a217f8 *R/writeBED.R
062cc1d6f4db9d37e7603e8235b66c02 *R/writeFASTA.R
fd438dc4f90761bcbcd7c2e11a46a5f3 *R/writeVCF.R
8395a2dd3f82634a5c03289e68d0bf4c *R/zzz.R
9ade3b04087662631d68e1d3793c8c6f *README.md
6f3939f14a39c2217e10f6a24872f9e9 *data/example_genome_coor.rda
738f9bb7d55a88a7df2db15f5a3d8a12 *data/example_kmertone_score.rda
c4a44f8868bf2dd1f5cad18245d03aa7 *inst/doc/kmeRtone.pdf
60b76bbafa1055f97733479413d7b7ee *man/Coordinate.Rd
70f71a01a21067d9d6b24897006c0cb7 *man/EXPLORE.Rd
4cc6a89a9ebfab1333a7554a6013f577 *man/Kmer_Table.Rd
88df260a3d697c6494b69eb1febeb9ce *man/NCBI_Genome.Rd
3173a196434eb0c1f53a0e7a14c6b181 *man/SCORE.Rd
bb8d65ecbc8e59f13c5682d3e9c8694d *man/STUDY_ACROSS_POPULATIONS.Rd
825c5f228d7a18a5b672868170fe65bd *man/STUDY_ACROSS_SPECIES.Rd
b09b1860458cd5033b13f4ff6a7ff278 *man/STUDY_CANCER_GENES.Rd
90b943871120a0719129320231c95436 *man/STUDY_GENIC_ELEMENTS.Rd
6842bb859d40c2f9e629e372d7fbc09c *man/UCSC_Genome.Rd
9a787b1137624a1143f252eb3728655c *man/addAlphaCol.Rd
bba6265a274332eeb28c1b13a1438db5 *man/bedToCoor.Rd
a972f57a268b83003ff0a752144dd246 *man/buildControl.Rd
b5123f2a18fad1e2c6962c0d302f7090 *man/buildKmerTable.Rd
036aa89f0a77d27bb7b2733031a4112e *man/buildMidPatternKmerTable.Rd
37186f02a7f2a4360d9a6f7de6fbe6c8 *man/buildRESTurl.Rd
afae8cf52e5b68225112b41d1205e6dd *man/buildRangedKmerTable.Rd
b4401a8b2381a6b0177ceca6c38a28ea *man/calKmerSkew.Rd
335b22cf635cdc0551cf355cb8c7e4e4 *man/calPWM.Rd
ce5ebf8445514f28ae7d7c6e042bd1c9 *man/catHeader.Rd
c893771c3be9ac2f21161c2eed4a9d08 *man/countBaseComposition.Rd
0f0e678c3d1c68a2801e5954984fd678 *man/countChoppedKmers.Rd
23e8ba50b17f162b215ea4ce12b044c6 *man/countDistribution.Rd
efd77e3474762ce61f72d0f95b0c633f *man/countKmers.Rd
84d9bdedd4595abf81a3f19faa17372a *man/countMidPatternContext2.Rd
53cd42508ffed63a32466b3c08b2cfd0 *man/countMidPatternKmers.Rd
500c486d4a183c2f4774834fedf7358c *man/countPointContext2.Rd
cca3e4594eb5cfcdeb20ab2703770bdc *man/countRangedKmers.Rd
24b52d3f4c72ebb1b2517d75838d29ff *man/countRevCompKmers.Rd
a8cf0b6504d2f9a462b01d4485b38b94 *man/countSlidingWindow.Rd
c21548fbfef6c875e629790d37fbe981 *man/countSlidingWindow2.Rd
f86b09c1aea5abf434d5f1ec15af8def *man/count_substring_fixed.Rd
6cbe5bb6f3ee2ef99890ec548230c2bd *man/count_substring_regex.Rd
9e0758360473ccaf801010374ff8c3dc *man/downloadNCBIGenomes.Rd
68400de8a286e6b9bd0f3948bc068a43 *man/downloadUCSCgenome.Rd
9c595fa1ae13873f94acec25d1405f88 *man/example_genome_coor.Rd
e71f24402a4cf20dcac3e77441864255 *man/example_kmeRtone_score.Rd
822fcce8041480fb5dc074c2e1d8b306 *man/extractKmers.Rd
781da86c83a9c6b9950813a4cbc604c0 *man/figures/KmeRtone_logo.png
3fb8600c511e19348878aed571502314 *man/figures/kmeRtone_1.0.pdf
d94e8b066d63f8dc861dafb05276bf9b *man/figures/manual.pdf
99d5c22e522fb14b2638ce08aee03ddd *man/generateGenicElementCoor.Rd
c880d632b38210ef967201a467603dfd *man/generateIntergenicCoor.Rd
aba71db4993c05f5e5aa9f595e07a120 *man/getCOSMICauthURL.Rd
882c7f2124dd892be391513ad249cb17 *man/getCOSMICcancerGeneCensus.Rd
ddc54a549e5104d516325da0e4048634 *man/getCOSMIClatestVersion.Rd
0e53a1a5146d3ff6073fbf43e0495576 *man/getCOSMICmutantExport.Rd
7b69089c251e2e215a3ca082df881903 *man/getEnsemblData.Rd
8bca21e7e388c069f57bc807b1e85596 *man/getEnsemblRegionFeatures.Rd
6fccbc94fdd747d5978c089b7b07788c *man/getEnsemblVariantFeatures.Rd
35beff7daa03d6f9dab8e51ccbb4ce44 *man/getEnsemblVariantFeatures_serial.Rd
134c191efc420100c02bb4d3d9c413d2 *man/getGnomADvariants.Rd
24aadc0936d9fd32476ae78665bd418c *man/getICTVvirusMetadataResource.Rd
651e4740a49d1296449419b17fbdcfd5 *man/getNCBIassemblySummary.Rd
44fe3faa9625c8fdf9e059d37224997f *man/getScores.Rd
b138691efb7ff0da6b46a19e6b3d0706 *man/getUCSCgenePredTable.Rd
14c5ad6d654e2d33abc2e1ca3ebbc012 *man/getVCFmetainfo.Rd
498ef91f61f364a16bddac8c34f9d8d5 *man/initKmerTable.Rd
45e4dc1afae697d327497d180edf367c *man/kmeRtone.Rd
8454279e9367c68e45bd2dba288c3fb4 *man/loadCoordinate.Rd
cd9bce34b4f31e5484b4dc294c0182c2 *man/loadGenome.Rd
7be3a1d930a2ff9c36d20c934ec8ff75 *man/loadGenomicContents.Rd
c7ab01bb8ef23cba656384fcc9928036 *man/mapKmers.Rd
c511292cf277048bdd69ba584eb8e570 *man/mergeCoordinate.Rd
3c3e7666ec12f073059951e364bf0b7e *man/mixColors.Rd
f70f2982bf62d5c2d7803244a8bf1907 *man/partitionCoordinate.Rd
e1ca256c2a6abbf0255c773c6f745bbd *man/persistentDownload.Rd
016db7cc98f7ea1023405021a45d2f38 *man/readBED.Rd
99a1ea4cbe224d76b47c36f56330ae64 *man/readFASTA.Rd
a37415ee37ae5471858c8e8a4c69eb9d *man/readVCF.Rd
1239814a1eea60ab7ba197cf6f986ad6 *man/readVCF2.Rd
8dc8c71b4969a120199295d42a43e95f *man/removeRegion.Rd
b3ed074148b98d77481a5a0168600706 *man/reverseComplement.Rd
dc6783a44755af8156fe66ffab0a0a97 *man/scoreKmers.Rd
8c69fbf5062b4370b1c9a880ab6d579b *man/selectGenomesForCrossSpeciesStudy.Rd
476227eedbbbd1a7e6c26f784d9d650e *man/selectRepresentativeFromASM.Rd
062005f6d993e8861b9a434470362909 *man/simulatePopulation.Rd
409158b8fe762e93de336e7ce69f9444 *man/splitFASTA.Rd
631d06b789c505cb9eb1862c14851114 *man/system3.Rd
759954923d64f44970d3c8a4d91b1c60 *man/trimCoordinate.Rd
05ab5e65995502f3aef9cc53d10179b7 *man/writeBED.Rd
f446c1f5df5b44a652d60c4eedc410b3 *man/writeFASTA.Rd
6e29a8ac49f4fe66cc67e1bb90fbad88 *man/writeVCF.Rd
1bed462309fb85684c704a60e3a4fcdf *src/Makevars
064c2d2fb50dd2cee7b47cbd95c4ccdf *src/RcppExports.cpp
d295d6e8c017c55a96dfcdf744340c3c *src/countKmers.cpp
43bf60af740ed15ab9b57fd6630953f3 *src/countMidPatternContext.cpp
deeea1efc40056580e0eb888acc522a4 *src/countMidPatternContext2.cpp
212a52093df7a540fa8a4f6fc16fa7d1 *src/countMidPatternKmers.cpp
dfadb61d64a01e647ae0b351cc277ea6 *src/countMidPatternRangedKmers.cpp
104b4522e7ea18443b20c8724dfad0d6 *src/countPointContext.cpp
27f48b51f1e25bbca372a139556c7e21 *src/countPointContext2.cpp
004fae28edb783d44df3953ea475deac *src/countRangedKmers.cpp
e0f39f8172f955f866120fd21edb4eed *src/countRangedKmers.h
2d59f4fbbe08c37c2a7ccd79801ee0c0 *src/countSlidingWindow.cpp
8e53e5f6848129d1ab7e08d1d3f4dc49 *src/countSlidingWindow2.cpp
586ed9d80f426e8656f7ed55cec4ea81 *src/count_substring_fixed.cpp
24d094e1aed17e5c778a46cca2009893 *src/count_substring_fixed.h
7ef31d18b03abd020f2a0e70cf291d7b *src/count_substring_regex.cpp
33a21bb66235f298f2226b09b0c70f25 *src/count_substring_regex.h
193fb5206367d0a89003e70fe0984292 *src/import_stringi.cpp
07384333f6ca92d9045646782f109cf3 *src/simulatePopulation.cpp
1f996d67acc665aa302cc7bcd02ac668 *tests/testthat.R
1cb99787701bee047e010cf8234c7516 *tests/testthat/test_score.R
