DECIPHER-package {DECIPHER} | R Documentation

## Tools for curating, analyzing, and manipulating biological sequences

### Description

DECIPHER is a software toolset that can be used for deciphering and managing biological sequences efficiently using the R statistical programming language. The program is designed to be used with non-destructive workflows for importing, maintaining, analyzing, manipulating, and exporting a massive amount of sequences.

### Details

Package: | DECIPHER
Type: | Package
Depends: | R (>= 3.5.0), Biostrings (>= 2.59.1), RSQLite (>= 1.1), stats, parallel
Imports: | methods, DBI, S4Vectors, IRanges, XVector
LinkingTo: | Biostrings, RSQLite, S4Vectors, IRanges, XVector
License: | GPL-3
LazyLoad: | yes

Index:

    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
    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
    Cophenetic               Compute cophenetic distances on dendrogram objects
    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 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 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 Distance Between Sequences
    ExtractGenes             Extract Predicted Genes from a Genome
    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
    Genes-class              Genes objects and accessors
    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
    IdTaxa                   Assign Sequences a Taxonomic Classification
    LearnNonCoding           Learn a Non-Coding RNA Model
    LearnTaxa                Train a Classifier for Assigning Taxonomy
    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
    MODELS                   Available Models of DNA Evolution
    NNLS                     Sequential Coordinate-wise Algorithm for the
                             Non-negative Least Squares Problem
    NonCoding                NonCoding Models for Common Non-Coding RNA Families
    NonCoding-class          NonCoding Objects and Methods
    OrientNucleotides        Orient Nucleotide Sequences
    PFASUM                   PFASUM Amino Acid Substitution Matrices
    PredictDBN               Predict RNA Secondary Structure in Dot-Bracket
                             Notation
    PredictHEC               Predict Protein Secondary Structure as Helix,
                             Beta-Sheet, or Coil
    Read Dendrogram          Read a Dendrogram from a Newick Formatted File
    RemoveGaps               Remove Gap Characters in Sequences
    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
    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
    TrimDNA                  Trims DNA Sequences to the High Quality Region
                             Between Patterns
    WriteDendrogram          Write a Dendrogram to Newick Format
    WriteGenes               Write Genes to a File

### Author(s)

Erik Wright

Maintainer: Erik Wright <eswright@pitt.edu>

[Package DECIPHER version 2.22.0 Index]