Database Enabled Code for Ideal Probe Hybridization Employing R


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Documentation for package ‘DECIPHER’ version 1.12.0

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DECIPHER-package Database Enabled Code for Ideal Probe Hybridization Employing R
Add2DB Add Data To A Database
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 Simulate Amplification of DNA by PCR
Array2Matrix Create a Matrix Representation of a Microarray
BrowseDB View A Database Table In A Web Browser
BrowseSequences View Sequences In A Web Browser
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
deltaGrules Free Energy of Hybridization of Probe/Target Quadruplets
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
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
MeltDNA Simulate Melting of DNA
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.