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