Database Enabled Code for Ideal Probe Hybridization Employing R


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Documentation for package ‘DECIPHER’ version 1.10.1

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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.