Package ‘DECIPHER’ September 28, 2021 Type Package Title Tools for curating, analyzing, and manipulating biological sequences Version 2.21.0 Date 2021-05-18 Author Erik Wright Maintainer Erik Wright <[email protected]> biocViews Clustering, Genetics, Sequencing, DataImport, Visualization, Microarray, QualityControl, qPCR, Alignment, WholeGenome, Microbiome, ImmunoOncology, GenePrediction Description A toolset for deciphering and managing biological sequences. Depends R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel Imports methods, DBI, S4Vectors, IRanges, XVector LinkingTo Biostrings, S4Vectors, IRanges, XVector License GPL-3 ByteCompile true git_url https://git.bioconductor.org/packages/DECIPHER git_branch master git_last_commit 7cad0ab git_last_commit_date 2021-05-19 Date/Publication 2021-09-28 R topics documented: DECIPHER-package . .3 AA_REDUCED . .6 Add2DB . .7 AdjustAlignment . .8 AlignDB . 10 1 2 R topics documented: AlignProfiles . 13 AlignSeqs . 17 AlignSynteny . 20 AlignTranslation . 21 AmplifyDNA . 23 Array2Matrix . 26 BrowseDB . 27 BrowseSeqs . 28 CalculateEfficiencyArray . 32 CalculateEfficiencyFISH . 34 CalculateEfficiencyPCR . 36 Codec . 38 ConsensusSequence . 39 Cophenetic . 42 CorrectFrameshifts . 43 CreateChimeras . 46 DB2Seqs . 48 deltaGrules . 50 deltaHrules . 51 deltaHrulesRNA . 52 deltaSrules . 53 deltaSrulesRNA . 54 DesignArray . 55 DesignPrimers . 57 DesignProbes . 61 DesignSignatures . 64 DetectRepeats . 68 DigestDNA . 71 Disambiguate . 72 DistanceMatrix . 73 ExtractGenes . 76 FindChimeras . 77 FindGenes . 80 FindNonCoding . 82 FindSynteny . 83 FormGroups . 85 Genes . 87 HEC_MI . 89 IdClusters . 90 IdConsensus . 94 IdentifyByRank . 95 IdLengths . 96 IdTaxa . 98 LearnNonCoding . 100 LearnTaxa . 102 MapCharacters . 106 MaskAlignment . 108 MeltDNA . 111 DECIPHER-package 3 MIQS............................................ 113 MODELS . 114 NNLS............................................ 115 NonCoding . 117 NonCodingRNA . 118 OrientNucleotides . 118 PFASUM . 120 PredictDBN . 121 PredictHEC . 125 ReadDendrogram . 127 RemoveGaps . 128 RESTRICTION_ENZYMES . 129 SearchDB . 130 Seqs2DB . 132 StaggerAlignment . 134 Synteny . 136 Taxa............................................. 139 TerminalChar . 141 TileSeqs . 142 TrainingSet_16S . 144 TrimDNA . 145 WriteDendrogram . 147 WriteGenes . 149 Index 151 DECIPHER-package Tools for curating, analyzing, and manipulating biological sequences Description DECIPHER is a software toolset that can be used for deciphering and managing biological se- quences efficiently using the R statistical programming language. The program is designed to be used with non-destructive workflows for importing, maintaining, analyzing, manipulating, and ex- porting a massive amount of sequences. Details Package: DECIPHER Type: Package Depends: R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel Imports: methods, DBI, S4Vectors, IRanges, XVector LinkingTo: Biostrings, RSQLite, S4Vectors, IRanges, XVector License: GPL-3 LazyLoad: yes 4 DECIPHER-package Index: AA_REDUCED Reduced amino acid alphabets Add2DB Add Data to a Database AdjustAlignment Improve An Existing Alignment By Adjusting Gap Placements AlignDB Align Two Sets of Aligned Sequences in a Sequence Database AlignProfiles Align Two Sets of Aligned Sequences AlignSeqs Align a Set of Unaligned Sequences AlignSynteny Pairwise Aligns Syntenic Blocks AlignTranslation Align Sequences By Their Amino Acid Translation AmplifyDNA Simulate Amplification of DNA by PCR Array2Matrix Create a Matrix Representation of a Microarray BrowseDB View a Database Table in a Web Browser BrowseSeqs View Sequences in a Web Browser CalculateEfficiencyArray Predict the Hybridization Efficiency of Probe/Target Sequence Pairs CalculateEfficiencyFISH Predict Thermodynamic Parameters of Probe/Target Sequence Pairs CalculateEfficiencyPCR Predict Amplification Efficiency of Primer Sequences Codec Compression/Decompression of Character Vectors ConsensusSequence Create a Consensus Sequence Cophenetic Compute cophenetic distances on dendrogram objects CorrectFrameshifts Corrects Frameshift Errors In Protein Coding Sequences CreateChimeras Create Artificial Chimeras DB2Seqs Export Database Sequences to a FASTA or FASTQ File deltaGrules Free Energy of Hybridization of Probe/Target Quadruplets deltaHrules Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution deltaHrulesRNA Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution deltaSrules Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution deltaSrulesRNA Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution DesignArray Design a Set of DNA Microarray Probes for Detecting Sequences DesignPrimers Design Primers Targeting a Specific Group of Sequences DesignProbes Design FISH Probes Targeting a Specific Group of Sequences DesignSignatures Design PCR Primers for Amplifying Group-Specific Signatures DetectRepeats Detect Repeats in a Sequence DigestDNA Simulate Restriction Digestion of DNA Disambiguate Expand Ambiguities into All Permutations of a DECIPHER-package 5 DNAStringSet DistanceMatrix Calculate the Distance Between Sequences ExtractGenes Extract Predicted Genes from a Genome FindChimeras Find Chimeras in a Sequence Database FindGenes Find Genes in a Genome FindNonCoding Find Non-Coding RNAs in a Genome FindSynteny Finds Synteny in a Sequence Database FormGroups Forms Groups By Rank Genes-class Genes objects and accessors HEC_MI Mutual Information for Protein Secondary Structure Prediction IdClusters Cluster Sequences By Distance or Sequence IdConsensus Create Consensus Sequences by Groups IdentifyByRank Identify.