DECIPHER-package |
Database Enabled Code for Ideal Probe Hybridization Employing R |
Add2DB |
Add Data To A Database |
AlignDB |
Aligns Two Sets of Aligned Sequences In A Sequence Database |
AlignProfiles |
Aligns Two Sets of Aligned Sequences |
AlignSeqs |
Aligns A Set of Unaligned Sequences |
AlignTranslation |
Aligns Sequences By Their Amino Acid Translation |
Array2Matrix |
Creates a Matrix Representation of a Microarray |
BrowseDB |
View A Database Table In A Web Browser |
BrowseSequences |
View Sequences In A Web Browser |
CalculateEfficiencyArray |
Predicts the Hybridization Efficiency of Probe/Target Sequence Pairs |
CalculateEfficiencyFISH |
Predicts Thermodynamic Parameters of Probe/Target Sequence Pairs |
CalculateEfficiencyPCR |
Predicts Amplification Efficiency of Primer Sequences |
ConsensusSequence |
Create A Consensus Sequence |
CreateChimeras |
Creates 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 |
Designs a set of DNA Microarray Probes for Detecting Sequences |
DesignPrimers |
Designs PCR Primers Targeting a Specific Group of Sequences |
DesignProbes |
Designs 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 |
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. |