DECIPHER-package |
Database Enabled Code for Ideal Probe Hybridization Employing R |
Add2DB |
Add Data To A Database |
AdjustAlignment |
Improve An Existing Alignment By Adjusting Gap Placements |
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 |
Deprecated functions in package 'DECIPHER' |
AmplifyDNA |
Simulate Amplification of DNA by PCR |
Array2Matrix |
Create a Matrix Representation of a Microarray |
BrowseDB |
View A Database Table In A Web Browser |
BrowseSeqs |
View Sequences In A Web Browser |
BrowseSequences |
Deprecated functions in package 'DECIPHER' |
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 |
DECIPHER-deprecated |
Deprecated functions in package 'DECIPHER' |
deltaGrules |
Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays |
deltaHrules |
Change in Enthalpy of Hybridization of Primer/Target Quadruplets in Solution |
deltaSrules |
Change in Entropy of Hybridization of Primer/Target Quadruplets in Solution |
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 |
DesignSignatures |
Design PCR Primers for Amplifying Group-Specific Signatures |
DigestDNA |
Simulate Restriction Digestion of DNA |
Disambiguate |
Expand Ambiguities into All Permutations of a DNAStringSet |
DistanceMatrix |
Calculate the Distances Between Sequences |
FindChimeras |
Find Chimeras In A Sequence Database |
FormGroups |
Forms Groups By Rank |
HEC_MI1 |
Mutual Information for Protein Secondary Structure Prediction |
HEC_MI2 |
Mutual Information for Protein Secondary Structure Prediction |
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 |
MIQS |
MIQS Amino Acid Substitution Matrix |
MODELS |
Available Models of DNA Evolution |
NNLS |
Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem |
PredictHEC |
Predict Protein Secondary Structure |
RESTRICTION_ENZYMES |
Common Restriction Enzyme's Cut Sites |
SearchDB |
Obtain Specific Sequences from A Database |
Seqs2DB |
Add Sequences from Text File to Database |
StaggerAlignment |
Produce a Staggered Alignment |
TerminalChar |
Determine the Number of Terminal Characters |
TileSeqs |
Form a Set of Tiles for Each Group of Sequences. |