# Database Enabled Code for Ideal Probe Hybridization Employing R

## Documentation for package ‘DECIPHER’ version 1.10.1

- 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
AlignDB | Aligns Two Sets of Aligned Sequences In A Sequence Database
AlignProfiles | Aligns Two Sets of Aligned Sequences
AlignSeqs | Aligns A Set of Unaligned Sequences
AlignTranslation | Aligns Sequences By Their Amino Acid Translation
Array2Matrix | Creates a Matrix Representation of a Microarray
BrowseDB | View A Database Table In A Web Browser
BrowseSequences | View Sequences In A Web Browser
CalculateEfficiencyArray | Predicts the Hybridization Efficiency of Probe/Target Sequence Pairs
CalculateEfficiencyFISH | Predicts Thermodynamic Parameters of Probe/Target Sequence Pairs
CalculateEfficiencyPCR | Predicts Amplification Efficiency of Primer Sequences
ConsensusSequence | Create A Consensus Sequence
CreateChimeras | Creates Artificial Chimeras
DB2Seqs | Export Database Sequences to a FASTA or FASTQ File
DECIPHER | Database Enabled Code for Ideal Probe Hybridization Employing R
deltaGrules | Free Energy of Hybridization of Probe/Target Quadruplets
DesignArray | Designs a set of DNA Microarray Probes for Detecting Sequences
DesignPrimers | Designs PCR Primers Targeting a Specific Group of Sequences
DesignProbes | Designs FISH Probes Targeting a Specific Group of Sequences
DistanceMatrix | Calculate the Distances Between Sequences
FindChimeras | Find Chimeras In A Sequence Database
FormGroups | Forms Groups By Rank
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
MODELS | Available Models of DNA Evolution
NNLS | Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
RESTRICTION_ENZYMES | Common Restriction Sites Named By Restriction Enzyme
SearchDB | Obtain Specific Sequences from A Database
Seqs2DB | Add Sequences from Text File to Database
TerminalChar | Determine the Number of Terminal Characters
TileSeqs | Form a Set of Tiles for Each Group of Sequences.