![]() )Ī DNAStringSet or RNAStringSet object of unaligned sequences. MaskAlignment: Mask Highly Variable Regions of An AlignmentĪlignTranslation ( myXStringSet, sense = "+", direction = "5' to 3'", readingFrame = NA, type = class ( myXStringSet ), geneticCode = GENETIC_CODE.MapCharacters: Map Changes in Ancestral Character States.LearnTaxa: Train a Classifier for Assigning Taxonomy.IdTaxa: Assign Sequences a Taxonomic Classification.IdLengths: Determine the Number of Bases, Nonbases, and Width of Each.IdentifyByRank: Identify By Taxonomic Rank.IdConsensus: Create Consensus Sequences by Groups.IdClusters: Cluster Sequences By Distance or Sequence. ![]() HEC_MI: Mutual Information for Protein Secondary Structure Prediction.Genes-class: Genes objects and accessors.FindSynteny: Finds Synteny in a Sequence Database.FindChimeras: Find Chimeras in a Sequence Database.ExtractGenes: Extract Predicted Genes from a Genome.DistanceMatrix: Calculate the Distances Between Sequences.Disambiguate: Expand Ambiguities into All Permutations of a DNAStringSet.DigestDNA: Simulate Restriction Digestion of DNA.DesignSignatures: Design PCR Primers for Amplifying Group-Specific Signatures.DesignProbes: Design FISH Probes Targeting a Specific Group of Sequences.DesignPrimers: Design PCR Primers Targeting a Specific Group of Sequences.DesignArray: Design a Set of DNA Microarray Probes for Detecting Sequences.deltaSrulesRNA: Change in Entropy of Hybridization of RNA/RNA Quadruplets in.deltaSrules: Change in Entropy of Hybridization of DNA/DNA Quadruplets in.deltaHrulesRNA: Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in.deltaHrules: Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in.deltaGrules: Free Energy of Hybridization of Probe/Target Quadruplets on.DECIPHER-package: Tools for curating, analyzing, and manipulating biological.DB2Seqs: Export Database Sequences to a FASTA or FASTQ File.CreateChimeras: Create Artificial Chimeras.CorrectFrameshifts: Corrects Frameshift Errors In Protein Coding Sequences.Cophenetic: Compute cophenetic distances on dendrogram objects.ConsensusSequence: Create a Consensus Sequence.Codec: Compression/Decompression of Character Vectors.CalculateEfficiencyPCR: Predict Amplification Efficiency of Primer Sequences.CalculateEfficiencyFISH: Predict Thermodynamic Parameters of Probe/Target Sequence.CalculateEfficiencyArray: Predict the Hybridization Efficiency of Probe/Target Sequence.BrowseSeqs: View Sequences in a Web Browser.BrowseDB: View a Database Table in a Web Browser.Array2Matrix: Create a Matrix Representation of a Microarray.AmplifyDNA: Simulate Amplification of DNA by PCR.AlignTranslation: Align Sequences By Their Amino Acid Translation.AlignSynteny: Pairwise Aligns Syntenic Blocks.AlignSeqs: Align a Set of Unaligned Sequences.AlignProfiles: Align Two Sets of Aligned Sequences.AlignDB: Align Two Sets of Aligned Sequences in a Sequence Database.AdjustAlignment: Improve An Existing Alignment By Adjusting Gap Placements.AA_REDUCED: Reduced amino acid alphabets.
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