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. |