Database Enabled Code for Ideal Probe Hybridization Employing R


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Documentation for package ‘DECIPHER’ version 1.14.5

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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.