Files in kmeRtone

Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

README.md R/RcppExports.R R/system3.R R/splitFASTA.R R/reverseComplement.R R/readBED.R R/selectGenomesForCrossSpeciesStudy.R R/precomputeGenomicContents.R R/getVCFmetainfo.R R/NCBI_Genome.R R/getICTVvirusMetadataResource.R R/STUDY_ACROSS_POPULATIONS.R R/getCOSMICauthURL.R R/partitionCoordinate.R R/getEnsemblVariantFeatures.R R/STUDY_CANCER_GENES.R R/mixColors.R R/getUCSCgenePredTable.R R/countBaseComposition.R R/SCORE.R R/example_genome_coor.R R/getCOSMIClatestVersion.R R/buildMidPatternKmerTable.R R/getNCBIassemblySummary.R R/readVCF2.R R/getEnsemblData.R R/scoreKmers.R R/getGnomADvariants.R R/getEnsemblRegionFeatures.R R/buildRangedKmerTable.R R/downloadNCBIGenomes.R R/removeRegion.R R/loadGenome.R R/pkg_attach.R R/bedToCoor.R R/countChoppedKmers.R R/mapKmers.R R/catHeader.R R/buildKmerTable.R R/generateGenicElementCoor.R R/Kmer_Table.R R/example_kmertone_score.R R/countDistribution.R R/extractKmers.R R/getEnsemblVariantFeatures_serial.R R/getScores.R R/loadCoordinate.R R/mergeCoordinate.R R/buildRESTurl.R R/writeFASTA.R R/downloadUCSCgenome.R R/generateIntergenicCoor.R R/STUDY_GENIC_ELEMENTS.R R/kmeRtone.R R/countRevCompKmers.R R/EXPLORE.R R/zzz.R R/readVCF.R R/persistentDownload.R R/getCOSMICcancerGeneCensus.R R/calPWM.R R/trimCoordinate.R R/STUDY_ACROSS_SPECIES.R R/buildControl.R R/addAlphaCol.R R/calKmerSkew.R R/writeVCF.R R/readFASTA.R R/initKmerTable.R R/writeBED.R R/selectRepresentativeFromASM.R R/UCSC_Genome.R R/Coordinate.R R/getCOSMICmutantExport.R inst/doc/kmeRtone.pdf tests/testthat.R tests/testthat/test_score.R man/buildRangedKmerTable.Rd man/NCBI_Genome.Rd man/splitFASTA.Rd man/countPointContext2.Rd man/writeFASTA.Rd man/removeRegion.Rd man/generateGenicElementCoor.Rd man/writeVCF.Rd man/mapKmers.Rd man/trimCoordinate.Rd man/Coordinate.Rd man/countMidPatternKmers.Rd man/buildKmerTable.Rd man/kmeRtone.Rd man/extractKmers.Rd man/mixColors.Rd man/UCSC_Genome.Rd man/system3.Rd man/countBaseComposition.Rd man/readFASTA.Rd man/getNCBIassemblySummary.Rd man/countMidPatternContext2.Rd man/count_substring_fixed.Rd man/countChoppedKmers.Rd man/getScores.Rd man/loadCoordinate.Rd man/STUDY_CANCER_GENES.Rd man/calKmerSkew.Rd man/buildMidPatternKmerTable.Rd man/mergeCoordinate.Rd man/getVCFmetainfo.Rd man/getCOSMICcancerGeneCensus.Rd man/countSlidingWindow.Rd man/getCOSMIClatestVersion.Rd man/example_genome_coor.Rd man/getGnomADvariants.Rd man/partitionCoordinate.Rd man/buildControl.Rd man/countSlidingWindow2.Rd man/selectRepresentativeFromASM.Rd man/getEnsemblRegionFeatures.Rd man/writeBED.Rd man/selectGenomesForCrossSpeciesStudy.Rd man/calPWM.Rd man/getEnsemblData.Rd man/STUDY_ACROSS_SPECIES.Rd man/reverseComplement.Rd man/bedToCoor.Rd man/countKmers.Rd man/getICTVvirusMetadataResource.Rd man/loadGenomicContents.Rd man/addAlphaCol.Rd man/getEnsemblVariantFeatures.Rd man/STUDY_ACROSS_POPULATIONS.Rd man/simulatePopulation.Rd man/readVCF2.Rd man/EXPLORE.Rd man/downloadUCSCgenome.Rd man/countDistribution.Rd man/persistentDownload.Rd man/downloadNCBIGenomes.Rd man/generateIntergenicCoor.Rd man/STUDY_GENIC_ELEMENTS.Rd man/initKmerTable.Rd man/getUCSCgenePredTable.Rd man/SCORE.Rd man/Kmer_Table.Rd man/example_kmeRtone_score.Rd man/getEnsemblVariantFeatures_serial.Rd man/readBED.Rd man/readVCF.Rd man/getCOSMICmutantExport.Rd man/getCOSMICauthURL.Rd man/countRevCompKmers.Rd man/buildRESTurl.Rd man/loadGenome.Rd man/countRangedKmers.Rd man/count_substring_regex.Rd man/scoreKmers.Rd man/catHeader.Rd man/figures/manual.pdf man/figures/kmeRtone_1.0.pdf