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DECIPHER (version 1.12.0)

Database Enabled Code for Ideal Probe Hybridization Employing R

Description

A toolset for deciphering and managing biological sequences.

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Version

Version

1.12.0

License

GPL-3

Maintainer

Erik Wright

Last Published

February 15th, 2017

Functions in DECIPHER (1.12.0)

Array2Matrix

Create a Matrix Representation of a Microarray
NNLS

Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
DesignProbes

Design FISH Probes Targeting a Specific Group of Sequences
BrowseDB

View A Database Table In A Web Browser
MODELS

Available Models of DNA Evolution
DistanceMatrix

Calculate the Distances Between Sequences
AlignProfiles

Align Two Sets of Aligned Sequences
AlignSeqs

Align A Set of Unaligned Sequences
Seqs2DB

Add Sequences from Text File to Database
TerminalChar

Determine the Number of Terminal Characters
Add2DB

Add Data To A Database
AlignDB

Align Two Sets of Aligned Sequences In A Sequence Database
DesignArray

Design a set of DNA Microarray Probes for Detecting Sequences
DesignPrimers

Design PCR Primers Targeting a Specific Group of Sequences
FindChimeras

Find Chimeras In A Sequence Database
FormGroups

Forms Groups By Rank
RESTRICTION_ENZYMES

Common Restriction Sites Named By Restriction Enzyme
SearchDB

Obtain Specific Sequences from A Database
CalculateEfficiencyPCR

Predict Amplification Efficiency of Primer Sequences
IdentifyByRank

Identify By Taxonomic Rank
ConsensusSequence

Create A Consensus Sequence
IdLengths

Determine the Number of Bases, Nonbases, and Width of Each Sequence
TileSeqs

Form a Set of Tiles for Each Group of Sequences.
BrowseSequences

View Sequences In A Web Browser
CalculateEfficiencyFISH

Predict Thermodynamic Parameters of Probe/Target Sequence Pairs
CreateChimeras

Create Artificial Chimeras
DB2Seqs

Export Database Sequences to a FASTA or FASTQ File
IdClusters

Cluster Sequences By Distance or Sequence
IdConsensus

Create Consensus Sequences by Groups
AlignTranslation

Align Sequences By Their Amino Acid Translation
DECIPHER-package

Database Enabled Code for Ideal Probe Hybridization Employing R
Amplify

Simulate Amplification of DNA by PCR
deltaGrules

Free Energy of Hybridization of Probe/Target Quadruplets
MaskAlignment

Masks Highly Variable Regions of An Alignment
MeltDNA

Simulate Melting of DNA