Tools for curating, analyzing, and manipulating biological sequences

Documentation for package ‘DECIPHER’ version 3.5.0

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Tools for curating, analyzing, and manipulating biological sequences

-- A --

AA_REDUCED	Reduced amino acid alphabets
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
AlignPairs	Align pairs of sequences
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
as.dist.Synteny	Synteny blocks and hits

-- B --

BLOSUM	BLOSUM Amino Acid Substitution Matrices
BrowseDB	View a Database Table in a Web Browser
BrowseSeqs	View Sequences in a Web Browser

-- C --

c.Taxa	Taxa training and testing objects
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
Clusterize	Cluster Sequences By Distance
Codec	Compression/Decompression of Character Vectors
ConsensusSequence	Create a Consensus Sequence
Cophenetic	Compute cophenetic distances on dendrogram objects
CorrectFrameshifts	Corrects Frameshift Errors In Protein Coding Sequences
CreateChimeras	Create Artificial Chimeras

-- D --

DB2Seqs	Export Database Sequences to a FASTA or FASTQ File
DECIPHER	Tools for curating, analyzing, and manipulating biological sequences
deltaGrules	Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays
deltaGrulesRNA	Pseudoenergy Parameters for RNA Quadruplets
deltaHrules	Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution
deltaHrulesRNA	Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution
deltaSrules	Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution
deltaSrulesRNA	Change in Entropy of Hybridization of RNA/RNA 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
DetectRepeats	Detect Repeats in a Sequence
DigestDNA	Simulate Restriction Digestion of DNA
Disambiguate	Expand Ambiguities into All Permutations of a DNAStringSet
DistanceMatrix	Calculate the Distances Between Sequences

-- E --

Extract Predicted Genes from a Genome

-- F --

FindChimeras	Find Chimeras in a Sequence Database
FindGenes	Find Genes in a Genome
FindNonCoding	Find Non-Coding RNAs in a Genome
FindSynteny	Finds Synteny in a Sequence Database
FormGroups	Forms Groups By Rank

-- G --

Genes objects and accessors

-- H --

HEC_MI1	Mutual Information for Protein Secondary Structure Prediction
HEC_MI2	Mutual Information for Protein Secondary Structure Prediction

-- I --

IdConsensus	Create Consensus Sequences by Groups
IdentifyByRank	Identify By Taxonomic Rank
IdLengths	Determine the Number of Characters in Each Sequence
IdTaxa	Assign Sequences a Taxonomic Classification
IndexSeqs	Build an inverted index
InferDemography	Infer Demographic History from Allele Frequencies
InferRecombination	Infer Recombination Parameters from Correlation Profiles
InferSelection	Infer Codon Selection on Protein Coding Sequences
InvertedIndex-class	InvertedIndex objects

-- L --

LearnNonCoding	Learn a Non-Coding RNA Model
LearnTaxa	Train a Classifier for Assigning Taxonomy

-- M --

MapCharacters	Map Changes in Ancestral Character States
MaskAlignment	Mask Highly Variable Regions of An Alignment
MeltDNA	Simulate Melting of DNA
MIQS	MIQS Amino Acid Substitution Matrix
MMLSUM	MMLSUM Amino Acid Substitution Matrices
MODELS	Available Models of Sequence Evolution

-- N --

NNLS	Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem
NonCoding-class	NonCoding Objects and Methods
NonCodingRNA_Archaea	NonCoding Models for Common Non-Coding RNA Families
NonCodingRNA_Bacteria	NonCoding Models for Common Non-Coding RNA Families
NonCodingRNA_Eukarya	NonCoding Models for Common Non-Coding RNA Families

-- O --

Orient Nucleotide Sequences

-- P --

pairs.Synteny	Synteny blocks and hits
PAM	PAM Amino Acid Substitution Matrices
PFASUM	PFASUM Amino Acid Substitution Matrices
plot.Genes	Genes objects and accessors
plot.Synteny	Synteny blocks and hits
plot.Taxa	Taxa training and testing objects
PredictDBN	Predict RNA Secondary Structure in Dot-Bracket Notation
PredictHEC	Predict Protein Secondary Structure
print.Genes	Genes objects and accessors
print.InvertedIndex	InvertedIndex objects
print.NonCoding	NonCoding Objects and Methods
print.Synteny	Synteny blocks and hits
print.Taxa	Taxa training and testing objects

-- R --

ReadDendrogram	Read a Dendrogram from a Newick Formatted File
RemoveGaps	Remove Gap Characters in Sequences
RESTRICTION_ENZYMES	Common Restriction Enzyme's Cut Sites

-- S --

ScoreAlignment	Score a Multiple Sequence Alignment
SearchDB	Obtain Specific Sequences from a Database
SearchIndex	Search an inverted index
Seqs2DB	Add Sequences from Text File to Database
StaggerAlignment	Produce a Staggered Alignment
Synteny-class	Synteny blocks and hits

-- T --

Taxa-class	Taxa training and testing objects
TerminalChar	Determine the Number of Terminal Characters
TileSeqs	Form a Set of Tiles for Each Group of Sequences.
TrainingSet_16S	Training Set for Classification of 16S rRNA Gene Sequences
TreeLine	Construct a Phylogenetic Tree
Treeline	Construct a Phylogenetic Tree
TrimDNA	Trims DNA Sequences to the High Quality Region Between Patterns

-- W --

WriteDendrogram	Write a Dendrogram to Newick Format
WriteGenes	Write Genes to a File

-- misc --

[.Genes	Genes objects and accessors
[.Synteny	Synteny blocks and hits
[.Taxa	Taxa training and testing objects