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| DECIPHER-package | Database Enabled Code for Ideal Probe Hybridization Employing R |
| 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 |
| AlignTranslation | Align Sequences By Their Amino Acid Translation |
| Amplify | Deprecated functions in package 'DECIPHER' |
| 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 |
| BrowseSequences | Deprecated functions in package 'DECIPHER' |
| 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 |
| ConsensusSequence | Create A Consensus Sequence |
| CreateChimeras | Create Artificial Chimeras |
| DB2Seqs | Export Database Sequences to a FASTA or FASTQ File |
| DECIPHER | Database Enabled Code for Ideal Probe Hybridization Employing R |
| DECIPHER-deprecated | Deprecated functions in package 'DECIPHER' |
| deltaGrules | Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays |
| deltaHrules | Change in Enthalpy of Hybridization of Primer/Target Quadruplets in Solution |
| deltaSrules | Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution |
| DesignArray | Design a set of DNA Microarray Probes for Detecting Sequences |
| DesignPrimers | Design PCR 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 |
| DigestDNA | Simulate Restriction Digestion of DNA |
| Disambiguate | Expand Ambiguities into All Permutations of a DNAStringSet |
| DistanceMatrix | Calculate the Distances Between Sequences |
| FindChimeras | Find Chimeras In A Sequence Database |
| FormGroups | Forms Groups By Rank |
| HEC_MI1 | Mutual Information for Protein Secondary Structure Prediction |
| HEC_MI2 | Mutual Information for Protein Secondary Structure Prediction |
| IdClusters | Cluster Sequences By Distance or Sequence |
| IdConsensus | Create Consensus Sequences by Groups |
| IdentifyByRank | Identify By Taxonomic Rank |
| IdLengths | Determine the Number of Bases, Nonbases, and Width of Each Sequence |
| MaskAlignment | Masks Highly Variable Regions of An Alignment |
| MeltDNA | Simulate Melting of DNA |
| MIQS | MIQS Amino Acid Substitution Matrix |
| MODELS | Available Models of DNA Evolution |
| NNLS | Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem |
| PredictHEC | Predict Protein Secondary Structure |
| RESTRICTION_ENZYMES | Common Restriction Enzyme's Cut Sites |
| SearchDB | Obtain Specific Sequences from A Database |
| Seqs2DB | Add Sequences from Text File to Database |
| StaggerAlignment | Produce a Staggered Alignment |
| TerminalChar | Determine the Number of Terminal Characters |
| TileSeqs | Form a Set of Tiles for Each Group of Sequences. |