Package: DECIPHER 3.9.0

Erik Wright

DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Authors:Erik Wright

DECIPHER_3.9.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DECIPHER/json (API)

# Install 'DECIPHER' in R:
install.packages('DECIPHER', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • BLOSUM - BLOSUM Amino Acid Substitution Matrices
  • 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
  • HEC_MI1 - Mutual Information for Protein Secondary Structure Prediction
  • HEC_MI2 - Mutual Information for Protein Secondary Structure Prediction
  • MIQS - MIQS Amino Acid Substitution Matrix
  • MMLSUM - MMLSUM Amino Acid Substitution Matrices
  • 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
  • PAM - PAM Amino Acid Substitution Matrices
  • PFASUM - PFASUM Amino Acid Substitution Matrices
  • RESTRICTION_ENZYMES - Common Restriction Enzyme's Cut Sites
  • TrainingSet_16S - Training Set for Classification of 16S rRNA Gene Sequences

On BioConductor:DECIPHER-3.9.0(bioc 3.24)DECIPHER-3.8.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

clusteringgeneticssequencingdataimportvisualizationmicroarrayqualitycontrolqpcralignmentwholegenomemicrobiomeimmunooncologygenepredictionphylogeneticscomparativegenomicsopenmp

9.84 score 21 packages 1.5k scripts 415 mentions 69 exports 9 dependencies

Last updated from:fe1126ce1b. Checks:12 ERROR, 2 OK. Indexed: yes.

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Exports:AA_REDUCEDAdd2DBAdjustAlignmentAlignDBAlignPairsAlignProfilesAlignSeqsAlignSyntenyAlignTranslationAmplifyDNAArray2MatrixBrowseDBBrowseSeqsCalculateEfficiencyArrayCalculateEfficiencyFISHCalculateEfficiencyPCRClusterizeCodecConsensusSequenceCopheneticCorrectFrameshiftsCreateChimerasDB2SeqsDesignArrayDesignPrimersDesignProbesDesignSignaturesDetectRepeatsDigestDNADisambiguateDistanceMatrixExtractGenesFindChimerasFindGenesFindNonCodingFindSyntenyFormGroupsIdConsensusIdentifyByRankIdLengthsIdTaxaIndexSeqsInferDemographyInferRecombinationInferSelectionLearnNonCodingLearnTaxaMapCharactersMaskAlignmentMeltDNAMODELSNNLSOrientNucleotidesPredictDBNPredictHECReadDendrogramRemoveGapsScoreAlignmentSearchDBSearchIndexSeqs2DBStaggerAlignmentTerminalCharTileSeqsTreelineTrimDNAWriteDendrogramWriteGenesZipline

Dependencies:BiocGenericsBiostringscrayonDBIgenericsIRangesS4VectorsSeqinfoXVector

Growing Phylogenetic Trees in R with Treeline
Introduction | Performance Considerations | Preparing the Input Data | Choosing a Method and Model of Evolution | Minimum Evolution Phylogenetic Trees | Maximum Likelihood Phylogenetic Trees | Maximum Parsimony Phylogenetic Trees | Calculating Bootstrap Support Values | More Examples of Manipulating Dendrograms | Inspecting the Inputs and Outputs | Exporting the Tree | Generating a Summary Tree | Session Information
Rendered fromGrowingTrees.Rnwusingutils::Sweave

Last update: 2026-04-27
Started: 2022-04-25

Population Genetics Inference in R
Introduction | Getting Started | Inferring Demography | Inferring Recombination | Inferring Selection | Session Information
Rendered fromPopulationGenetics.Rnwusingutils::Sweave

Last update: 2026-03-22
Started: 2025-04-03

Getting Started DECIPHERing
About DECIPHER | Design Philosophy | Installation | Getting help | Functionality
Rendered fromDECIPHERing.Rnwusingutils::Sweave

Last update: 2025-10-14
Started: 2013-11-01

Searching Biological Sequences for Research
Introduction | Getting Started | Searching for hits between pattern and subject sequences | Aligning the search hits between pattern and subject | Controlling for false discoveries | Maximizing search sensitivity to find distant hits | Mapping long reads to a genome | Recommended search settings | Session Information
Rendered fromSearchForResearch.Rnwusingutils::Sweave

Last update: 2025-04-07
Started: 2024-02-11

Classify Sequences in R
Introduction | Getting Started | Training the Classifier | Classifying Sequences | Creating a ``taxid'' file | Annotating Protein Sequences | Session Information
Rendered fromClassifySequences.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2017-10-24

Design Group-Specific FISH Probes in R
Introduction | The Objective of FISH Probe Design | Getting Started | Probe Design Steps | Dual Probe Design Steps | Session Information
Rendered fromDesignProbes.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2013-11-01

Design Group-Specific Primers in R
Introduction | The Objective of Primer Design | Getting Started | Primer Design Steps | Additional Primer Analysis | Session Information
Rendered fromDesignPrimers.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2013-11-01

Design Microarray Probes in R
Introduction | Getting Started | Array Design and Validation Steps | Session Information
Rendered fromDesignMicroarray.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2013-11-01

Detecting Obscure Tandem Repeats in Sequences
Introduction | Getting Started | Taking a first look at Obscurin | Detecting repeats automatically with DetectRepeats | Inferring the History of Repeats in Obscurin | Session Information
Rendered fromRepeatRepeat.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2022-04-25

Finding Chimeric Sequences in R
Introduction | Chimera Finding Problems | Getting Started | Obtaining/Building A Reference Database | Steps to Find Chimeras | Session Information
Rendered fromFindChimeras.Rnwusingutils::Sweave

Last update: 2025-04-03
Started: 2013-11-01

Upsize Your Clustering with Clusterize
Introduction to supersized clustering | Getting started with Clusterize | Optimize your inputs to Clusterize | Visualize the output of Clusterize | Specialize clustering for your goals | Resize to fit within less memory | Clustering both nucleotide strands | Alternative measures of distance | Finalize your use of Clusterize
Rendered fromClusteringSequences.Rnwusingutils::Sweave

Last update: 2025-03-08
Started: 2022-09-15

Design Primers that Yield Group-Specific Signatures
Introduction | Getting Started | Designing primers with diverse signatures | Assessing the Results | Session Information
Rendered fromDesignSignatures.Rnwusingutils::Sweave

Last update: 2024-12-20
Started: 2015-09-23

The Double Life of RNA: Uncovering Non-Coding RNAs
Introduction | Getting Started | Building a Non-Coding RNA Model | Finding Non-Coding RNAs | Session Information
Rendered fromFindingNonCodingRNAs.Rnwusingutils::Sweave

Last update: 2024-11-29
Started: 2021-02-13

The Art of Multiple Sequence Alignment in R
Introduction | Alignment Speed | Alignment Accuracy | Recommendations for optimal performance | Single Gene Alignment | Advanced Options & Features | Aligning Homologous Regions of Multiple Genomes | Session Information
Rendered fromArtOfAlignmentInR.Rnwusingutils::Sweave

Last update: 2024-04-29
Started: 2014-01-26

The Magic of Gene Finding
Introduction | Getting Started | Finding Genes in a Genome | Analyzing the Output | Incorporating non-coding RNAs | Annotating the protein coding genes | Guaranteeing repeatability | Exporting the output | Session Information
Rendered fromFindingGenes.Rnwusingutils::Sweave

Last update: 2024-01-17
Started: 2020-10-26

Readme and manuals

Help Manual

Help pageTopics
Tools for curating, analyzing, and manipulating biological sequencesDECIPHER-package DECIPHER
Reduced amino acid alphabetsAA_REDUCED
Add Data to a DatabaseAdd2DB
Improve An Existing Alignment By Adjusting Gap PlacementsAdjustAlignment
Align Two Sets of Aligned Sequences in a Sequence DatabaseAlignDB
Align pairs of sequencesAlignPairs
Align Two Sets of Aligned SequencesAlignProfiles
Align a Set of Unaligned SequencesAlignSeqs
Pairwise Aligns Syntenic BlocksAlignSynteny
Align Sequences By Their Amino Acid TranslationAlignTranslation
Simulate Amplification of DNA by PCRAmplifyDNA
Create a Matrix Representation of a MicroarrayArray2Matrix
BLOSUM Amino Acid Substitution MatricesBLOSUM
View a Database Table in a Web BrowserBrowseDB
View Sequences in a Web BrowserBrowseSeqs
Predict the Hybridization Efficiency of Probe/Target Sequence PairsCalculateEfficiencyArray
Predict Thermodynamic Parameters of Probe/Target Sequence PairsCalculateEfficiencyFISH
Predict Amplification Efficiency of Primer SequencesCalculateEfficiencyPCR
Cluster Sequences By DistanceClusterize
Compression/Decompression of Character VectorsCodec
Create a Consensus SequenceConsensusSequence
Compute cophenetic distances on dendrogram objectsCophenetic
Corrects Frameshift Errors In Protein Coding SequencesCorrectFrameshifts
Create Artificial ChimerasCreateChimeras
Export Database Sequences to a FASTA or FASTQ FileDB2Seqs
Free Energy of Hybridization of Probe/Target Quadruplets on MicroarraysdeltaGrules
Pseudoenergy Parameters for RNA QuadrupletsdeltaGrulesRNA
Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in SolutiondeltaHrules
Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in SolutiondeltaHrulesRNA
Change in Entropy of Hybridization of DNA/DNA Quadruplets in SolutiondeltaSrules
Change in Entropy of Hybridization of RNA/RNA Quadruplets in SolutiondeltaSrulesRNA
Design a Set of DNA Microarray Probes for Detecting SequencesDesignArray
Design PCR Primers Targeting a Specific Group of SequencesDesignPrimers
Design FISH Probes Targeting a Specific Group of SequencesDesignProbes
Design PCR Primers for Amplifying Group-Specific SignaturesDesignSignatures
Detect Repeats in a SequenceDetectRepeats
Simulate Restriction Digestion of DNADigestDNA
Expand Ambiguities into All Permutations of a DNAStringSetDisambiguate
Calculate the Distances Between SequencesDistanceMatrix
Extract Predicted Genes from a GenomeExtractGenes
Find Chimeras in a Sequence DatabaseFindChimeras
Find Genes in a GenomeFindGenes
Find Non-Coding RNAs in a GenomeFindNonCoding
Finds Synteny in a Sequence DatabaseFindSynteny
Forms Groups By RankFormGroups
Genes objects and accessorsGenes-class plot.Genes print.Genes [.Genes
Mutual Information for Protein Secondary Structure PredictionHEC_MI1 HEC_MI2
Create Consensus Sequences by GroupsIdConsensus
Identify By Taxonomic RankIdentifyByRank
Determine the Number of Characters in Each SequenceIdLengths
Assign Sequences a Taxonomic ClassificationIdTaxa
Build an inverted indexIndexSeqs
Infer Demographic History from Allele FrequenciesInferDemography
Infer Recombination Parameters from Correlation ProfilesInferRecombination
Infer Codon Selection on Protein Coding SequencesInferSelection
InvertedIndex objectsInvertedIndex-class print.InvertedIndex
Learn a Non-Coding RNA ModelLearnNonCoding
Train a Classifier for Assigning TaxonomyLearnTaxa
Map Changes in Ancestral Character StatesMapCharacters
Mask Highly Variable Regions of An AlignmentMaskAlignment
Simulate Melting of DNAMeltDNA
MIQS Amino Acid Substitution MatrixMIQS
MMLSUM Amino Acid Substitution MatricesMMLSUM
Available Models of Sequence EvolutionMODELS
Sequential Coordinate-wise Algorithm for the Non-negative Least Squares ProblemNNLS
NonCoding Objects and MethodsNonCoding-class print.NonCoding
NonCoding Models for Common Non-Coding RNA FamiliesNonCodingRNA_Archaea NonCodingRNA_Bacteria NonCodingRNA_Eukarya
Orient Nucleotide SequencesOrientNucleotides
PAM Amino Acid Substitution MatricesPAM
PFASUM Amino Acid Substitution MatricesPFASUM
Predict RNA Secondary Structure in Dot-Bracket NotationPredictDBN
Predict Protein Secondary StructurePredictHEC
Read a Dendrogram from a Newick Formatted FileReadDendrogram
Remove Gap Characters in SequencesRemoveGaps
Common Restriction Enzyme's Cut SitesRESTRICTION_ENZYMES
Score a Multiple Sequence AlignmentScoreAlignment
Obtain Specific Sequences from a DatabaseSearchDB
Search an inverted indexSearchIndex
Add Sequences from Text File to DatabaseSeqs2DB
Produce a Staggered AlignmentStaggerAlignment
Synteny blocks and hitsas.dist.Synteny pairs.Synteny plot.Synteny print.Synteny Synteny-class [.Synteny
Taxa training and testing objectsc.Taxa plot.Taxa print.Taxa Taxa-class [.Taxa
Determine the Number of Terminal CharactersTerminalChar
Form a Set of Tiles for Each Group of Sequences.TileSeqs
Training Set for Classification of 16S rRNA Gene SequencesTrainingSet_16S
Construct a Phylogenetic TreeTreeLine Treeline
Trims DNA Sequences to the High Quality Region Between PatternsTrimDNA
Write a Dendrogram to Newick FormatWriteDendrogram
Write Genes to a FileWriteGenes
Summarize Multiple Phylogenetic TreesZipline