| Package: |
| DECIPHER |
| Type: |
| Package |
| Depends: |
| R (>= 2.13.0), Biostrings (>= 2.35.12), RSQLite (>= 1.0), stats, parallel |
| Imports: |
| methods, DBI, S4Vectors, IRanges, XVector |
| LinkingTo: |
| Biostrings, RSQLite, S4Vectors, IRanges, XVector |
| License: |
| GPL-3 |
| LazyLoad: |
| yes |
Index:
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
AlignSynteny Pairwise Aligns Syntenic Blocks
AlignTranslation Align Sequences By Their Amino Acid Translation
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
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
Codec Compression/Decompression of Character Vectors
ConsensusSequence Create a Consensus Sequence
CorrectFrameshifts Corrects Frameshift Errors In Protein Coding
Sequences
CreateChimeras Create Artificial Chimeras
DB2Seqs Export Database Sequences to a FASTA or FASTQ File
deltaGrules Free Energy of Hybridization of Probe/Target
Quadruplets
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 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 Distance Between Sequences
FindChimeras Find Chimeras in a Sequence Database
FindSynteny Finds Synteny in a Sequence Database
FormGroups Forms Groups By Rank
HEC_MI 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 Mask 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
OrientNucleotides Orient nucleotide sequences
PredictHEC Predict Protein Secondary Structure
Read Dendrogram Read a Dendrogram from a Newick Formatted File
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
Synteny-class Synteny blocks and hits
TerminalChar Determine the Number of Terminal Characters
TileSeqs Form a Set of Tiles for Each Group of Sequences
WriteDendrogram Write a Dendrogram to Newick Format