# Database Enabled Code for Ideal Probe Hybridization Employing R

## Documentation for package ‘DECIPHER’ version 1.14.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.