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DECIPHER (version 1.14.5)
Database Enabled Code for Ideal Probe Hybridization Employing R
Description
A toolset for deciphering and managing biological sequences.
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Version
Version
2.0.2
1.16.0
1.14.5
1.12.0
Version
1.14.5
License
GPL-3
Maintainer
Erik Wright
Last Published
February 15th, 2017
Functions in DECIPHER (1.14.5)
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BrowseDB
View A Database Table In A Web Browser
DistanceMatrix
Calculate the Distances Between Sequences
BrowseSeqs
View Sequences In A Web Browser
CalculateEfficiencyFISH
Predict Thermodynamic Parameters of Probe/Target Sequence Pairs
CalculateEfficiencyPCR
Predict Amplification Efficiency of Primer Sequences
IdClusters
Cluster Sequences By Distance or Sequence
FindChimeras
Find Chimeras In A Sequence Database
AlignDB
Align Two Sets of Aligned Sequences In A Sequence Database
AlignProfiles
Align Two Sets of Aligned Sequences
FormGroups
Forms Groups By Rank
HEC_MI
Mutual Information for Protein Secondary Structure Prediction
IdConsensus
Create Consensus Sequences by Groups
TerminalChar
Determine the Number of Terminal Characters
TileSeqs
Form a Set of Tiles for Each Group of Sequences.
SearchDB
Obtain Specific Sequences from A Database
RESTRICTION_ENZYMES
Common Restriction Enzyme's Cut Sites
Array2Matrix
Create a Matrix Representation of a Microarray
AmplifyDNA
Simulate Amplification of DNA by PCR
DB2Seqs
Export Database Sequences to a FASTA or FASTQ File
DECIPHER-deprecated
Deprecated functions in package ‘DECIPHER’
DesignArray
Design a set of DNA Microarray Probes for Detecting Sequences
DesignPrimers
Design PCR Primers Targeting a Specific Group of Sequences
NNLS
Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
Add2DB
Add Data To A Database
AdjustAlignment
Improve An Existing Alignment By Adjusting Gap Placements
CreateChimeras
Create Artificial Chimeras
ConsensusSequence
Create A Consensus Sequence
MIQS
MIQS Amino Acid Substitution Matrix
MODELS
Available Models of DNA Evolution
deltaHrules
Change in Enthalpy of Hybridization of Primer/Target Quadruplets in Solution
DigestDNA
Simulate Restriction Digestion of DNA
deltaSrules
Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution
Disambiguate
Expand Ambiguities into All Permutations of a DNAStringSet
Seqs2DB
Add Sequences from Text File to Database
StaggerAlignment
Produce a Staggered Alignment
IdentifyByRank
Identify By Taxonomic Rank
IdLengths
Determine the Number of Bases, Nonbases, and Width of Each Sequence
PredictHEC
Predict Protein Secondary Structure
AlignSeqs
Align A Set of Unaligned Sequences
AlignTranslation
Align Sequences By Their Amino Acid Translation
DECIPHER-package
Database Enabled Code for Ideal Probe Hybridization Employing R
deltaGrules
Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays
DesignProbes
Design FISH Probes Targeting a Specific Group of Sequences
DesignSignatures
Design PCR Primers for Amplifying Group-Specific Signatures
MaskAlignment
Masks Highly Variable Regions of An Alignment
MeltDNA
Simulate Melting of DNA