Files in DECIPHER
Tools for curating, analyzing, and manipulating biological sequences
NAMESPACE
DESCRIPTION
build/vignette.rds
src/InformationContent.c
src/GetPools.c
src/GeneFinding.c
src/MeltPolymer.c
src/Order.c
src/Translate.c
src/Diff.c
src/CalculateDeltaG.c
src/AlignProfiles.c
src/VectorSums.c
src/IntDist.c
src/Compression.c
src/Cluster.c
src/Compositions.c
src/TerminalMismatch.c
src/CalculateFISH.c
src/R_init_decipher.c
src/MultiMatch.c
src/EnumerateSequence.c
src/NNLS.c
src/PredictDBN.c
src/PredictHEC.c
src/Makevars
src/S4Vectors_stubs.c
src/MovingAverage.c
src/ConsolidateGaps.c
src/XVector_stubs.c
src/RemoveGaps.c
src/ReplaceChars.c
src/FindFrameshifts.c
src/ClusterML.c
src/ConsensusSequence.c
src/AssignIndels.c
src/DistanceMatrix.c
src/CommonGaps.c
src/ChainSegments.c
src/InsertGaps.c
src/Biostrings_stubs.c
src/ExpandAmbiguities.c
src/DesignProbes.c
src/DECIPHER.h
src/Import.c
data/deltaSrulesRNA.RData
data/deltaHrules.RData
data/RESTRICTION_ENZYMES.RData
data/TrainingSet_16S.RData
data/datalist
data/HEC_MI2.RData
data/deltaGrules.RData
data/HEC_MI1.RData
data/MIQS.RData
data/deltaSrules.RData
data/PFASUM.RData
data/deltaHrulesRNA.RData
R/PredictDBN.R
R/IdentifyByRank.R
R/Cophenetic.R
R/DesignArray.R
R/Synteny-class.R
R/AlignProfiles.R
R/Codec.R
R/Genes-class.R
R/ConsensusSequence.R
R/DB2Seqs.R
R/BrowseSeqs.R
R/DigestDNA.R
R/AmplifyDNA.R
R/FindSynteny.R
R/NNLS.R
R/Disambiguate.R
R/Taxa-class.R
R/utils.R
R/RemoveGaps.R
R/TrimDNA.R
R/ExtractGenes.R
R/FindGenes.R
R/LearnTaxa.R
R/StaggerAlignment.R
R/Add2DB.R
R/MaskAlignment.R
R/CalculateEfficiencyArray.R
R/WriteGenes.R
R/MeltDNA.R
R/CalculateEfficiencyPCR.R
R/MapCharacters.R
R/WriteDendrogram.R
R/PredictHEC.R
R/ReadDendrogram.R
R/TileSeqs.R
R/IdClusters.R
R/DesignSignatures.R
R/AA_REDUCED.R
R/OrientNucleotides.R
R/SearchDB.R
R/DistanceMatrix.R
R/FormGroups.R
R/IdTaxa.R
R/BrowseDB.R
R/zzz.R
R/AlignDB.R
R/FindChimeras.R
R/IdConsensus.R
R/AdjustAlignment.R
R/TerminalChar.R
R/AlignSeqs.R
R/CalculateEfficiencyFISH.R
R/AlignTranslation.R
R/CorrectFrameshifts.R
R/DesignProbes.R
R/Array2Matrix.R
R/CreateChimeras.R
R/DesignPrimers.R
R/Seqs2DB.R
R/AlignSynteny.R
R/IdLengths.R
vignettes/DenaturationPlot.pdf
vignettes/DesignSignatures.Rnw
vignettes/AlignmentBenchmarks.pdf
vignettes/DesignProbes.Rnw
vignettes/DesignPrimers.Rnw
vignettes/ClassifySequences.Rnw
vignettes/FormamideCurve.png
vignettes/FindChimeras.Rnw
vignettes/AmpliconSignatures.pdf
vignettes/BrowseProbesOutput.png
vignettes/DefaultVsChainedGuideTrees.pdf
vignettes/BrowseSignaturesOutput.png
vignettes/DECIPHERing.Rnw
vignettes/AlignmentFlowChart.pdf
vignettes/HOMSTRAD-modBenchmarkResults.pdf
vignettes/ArtOfAlignmentInR.Rnw
vignettes/DesignMicroarray.Rnw
vignettes/DualProbesScores.png
vignettes/DigestedSignatures.pdf
vignettes/BrowseDBOutput.png
vignettes/BrowseAmpliconOutput.png
vignettes/FindingGenes.Rnw
vignettes/AlignmentSpace2.png
vignettes/AlignmentSpace1.png
vignettes/BrowseSeqsOutput.png
man/IdTaxa.Rd
man/ReadDendrogram.Rd
man/AlignSynteny.Rd
man/DECIPHER-package.Rd
man/TerminalChar.Rd
man/TrainingSet_16S.Rd
man/Disambiguate.Rd
man/MeltDNA.Rd
man/AlignDB.Rd
man/TrimDNA.Rd
man/Seqs2DB.Rd
man/AlignSeqs.Rd
man/DesignPrimers.Rd
man/deltaHrules.Rd
man/BrowseDB.Rd
man/DistanceMatrix.Rd
man/WriteDendrogram.Rd
man/DB2Seqs.Rd
man/MODELS.Rd
man/FindGenes.Rd
man/deltaHrulesRNA.Rd
man/MapCharacters.Rd
man/Synteny-class.Rd
man/MaskAlignment.Rd
man/RemoveGaps.Rd
man/AdjustAlignment.Rd
man/DigestDNA.Rd
man/CreateChimeras.Rd
man/Cophenetic.Rd
man/IdLengths.Rd
man/deltaSrulesRNA.Rd
man/FindChimeras.Rd
man/AmplifyDNA.Rd
man/deltaGrules.Rd
man/deltaSrules.Rd
man/WriteGenes.Rd
man/Codec.Rd
man/RESTRICTION_ENZYMES.Rd
man/PredictHEC.Rd
man/CalculateEfficiencyArray.Rd
man/IdConsensus.Rd
man/StaggerAlignment.Rd
man/PredictDBN.Rd
man/ExtractGenes.Rd
man/IdClusters.Rd
man/TileSeqs.Rd
man/DesignSignatures.Rd
man/PFASUM.Rd
man/DesignArray.Rd
man/DesignProbes.Rd
man/NNLS.Rd
man/IdentifyByRank.Rd
man/BrowseSeqs.Rd
man/AlignTranslation.Rd
man/CorrectFrameshifts.Rd
man/SearchDB.Rd
man/OrientNucleotides.Rd
man/ConsensusSequence.Rd
man/FindSynteny.Rd
man/Genes-class.Rd
man/CalculateEfficiencyFISH.Rd
man/Taxa-class.Rd
man/Add2DB.Rd
man/Array2Matrix.Rd
man/MIQS.Rd
man/CalculateEfficiencyPCR.Rd
man/AlignProfiles.Rd
man/AA_REDUCED.Rd
man/HEC_MI.Rd
man/FormGroups.Rd
man/LearnTaxa.Rd
inst/CITATION
inst/doc/DesignSignatures.Rnw
inst/doc/DesignPrimers.pdf
inst/doc/DesignProbes.Rnw
inst/doc/DesignPrimers.Rnw
inst/doc/ClassifySequences.Rnw
inst/doc/FindChimeras.Rnw
inst/doc/ArtOfAlignmentInR.pdf
inst/doc/DECIPHERing.R
inst/doc/DesignProbes.pdf
inst/doc/DesignMicroarray.R
inst/doc/DECIPHERing.Rnw
inst/doc/ClassifySequences.pdf
inst/doc/DECIPHERing.pdf
inst/doc/ArtOfAlignmentInR.Rnw
inst/doc/DesignSignatures.R
inst/doc/DesignMicroarray.Rnw
inst/doc/FindChimeras.R
inst/doc/FindChimeras.pdf
inst/doc/DesignMicroarray.pdf
inst/doc/ArtOfAlignmentInR.R
inst/doc/ClassifySequences.R
inst/doc/DesignProbes.R
inst/doc/DesignSignatures.pdf
inst/doc/DesignPrimers.R
inst/doc/FindingGenes.Rnw
inst/doc/FindingGenes.pdf
inst/doc/FindingGenes.R
inst/extdata/Bacteria_175seqs.fas
inst/extdata/PlanctobacteriaNamedGenes.fas.gz
inst/extdata/Bacteria_175seqs.sqlite
inst/extdata/Bacteria_175seqs.gen
inst/extdata/IDH2.fas
inst/extdata/50S_ribosomal_protein_L2.fas
inst/extdata/Chlamydia_trachomatis_NC_000117.fas.gz
inst/extdata/Influenza.sqlite
inst/extdata/Streptomyces_ITS_aligned.fas
