Package: DECIPHER 3.3.2

Erik Wright

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

A toolset for deciphering and managing biological sequences.

Authors:Erik Wright

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DECIPHER.pdf |DECIPHER.html✨
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
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
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

On BioConductor:DECIPHER-3.3.1(bioc 3.21)DECIPHER-3.2.0(bioc 3.20)

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

clustering genetics sequencing dataimport visualization microarray qualitycontrol qpcr alignment wholegenome microbiome immunooncology geneprediction openmp

10.50 score 13 packages 892 scripts 4.4k downloads 415 mentions 67 exports 20 dependencies

Last updated 9 hours agofrom:c3647f8b29. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 20 2024
R-4.5-win-x86_64	NOTE	Dec 20 2024
R-4.5-linux-x86_64	NOTE	Dec 20 2024
R-4.4-win-x86_64	NOTE	Dec 20 2024
R-4.4-mac-x86_64	NOTE	Dec 20 2024
R-4.4-mac-aarch64	NOTE	Dec 20 2024
R-4.3-win-x86_64	NOTE	Dec 20 2024
R-4.3-mac-x86_64	NOTE	Dec 20 2024
R-4.3-mac-aarch64	NOTE	Dec 20 2024

Exports:AA_REDUCED Add2DB AdjustAlignment AlignDB AlignPairs AlignProfiles AlignSeqs AlignSynteny AlignTranslation AmplifyDNA Array2Matrix BrowseDB BrowseSeqs CalculateEfficiencyArray CalculateEfficiencyFISH CalculateEfficiencyPCR Clusterize Codec ConsensusSequence Cophenetic CorrectFrameshifts CreateChimeras DB2Seqs DesignArray DesignPrimers DesignProbes DesignSignatures DetectRepeats DigestDNA Disambiguate DistanceMatrix ExtractGenes FindChimeras FindGenes FindNonCoding FindSynteny FormGroups IdConsensus IdentifyByRank IdLengths IdTaxa IndexSeqs InferRecombination LearnNonCoding LearnTaxa MapCharacters MaskAlignment MeltDNA MODELS NNLS OrientNucleotides PredictDBN PredictHEC ReadDendrogram RemoveGaps ScoreAlignment SearchDB SearchIndex Seqs2DB StaggerAlignment TerminalChar TileSeqs Treeline TreeLine TrimDNA WriteDendrogram WriteGenes

Dependencies:askpass BiocGenerics Biostrings crayon curl DBI generics GenomeInfoDb GenomeInfoDbData httr IRanges jsonlite mime openssl R6 S4Vectors sys UCSC.utils XVector zlibbioc

Classify Sequences

Rendered fromClassifySequences.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-11-29
Started: 2017-10-24

Design Group-Specific FISH Probes

Rendered fromDesignProbes.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-11-29
Started: 2013-11-01

Design Group-Specific Primers

Rendered fromDesignPrimers.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-11-29
Started: 2013-11-01

Design Microarray Probes

Rendered fromDesignMicroarray.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-10-28
Started: 2013-11-01

Design Primers that Yield Group-Specific Signatures

Rendered fromDesignSignatures.Rnwusingutils::Sweaveon Dec 20 2024.

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

Detecting Obscure Tandem Repeats in Sequences

Rendered fromRepeatRepeat.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-12-20
Started: 2022-04-25

Finding Chimeric Sequences

Rendered fromFindChimeras.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-10-28
Started: 2013-11-01

Getting Started DECIPHERing

Rendered fromDECIPHERing.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-12-20
Started: 2013-11-01

Growing Phylogenetic Trees with Treeline

Rendered fromGrowingTrees.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-12-20
Started: 2022-04-25

Searching biological sequences

Rendered fromSearchForResearch.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-10-18
Started: 2024-02-11

The Art of Multiple Sequence Alignment in R

Rendered fromArtOfAlignmentInR.Rnwusingutils::Sweaveon Dec 20 2024.

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

The Double Life of RNA: Uncovering Non-Coding RNAs

Rendered fromFindingNonCodingRNAs.Rnwusingutils::Sweaveon Dec 20 2024.

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

The Magic of Gene Finding

Rendered fromFindingGenes.Rnwusingutils::Sweaveon Dec 20 2024.

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

Upsize Your Clustering with Clusterize

Rendered fromClusteringSequences.Rnwusingutils::Sweaveon Dec 20 2024.

Last update: 2024-10-28
Started: 2022-09-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for curating, analyzing, and manipulating biological sequences	DECIPHER-package DECIPHER
Reduced amino acid alphabets	AA_REDUCED
Add Data to a Database	Add2DB
Improve An Existing Alignment By Adjusting Gap Placements	AdjustAlignment
Align Two Sets of Aligned Sequences in a Sequence Database	AlignDB
Align pairs of sequences	AlignPairs
Align Two Sets of Aligned Sequences	AlignProfiles
Align a Set of Unaligned Sequences	AlignSeqs
Pairwise Aligns Syntenic Blocks	AlignSynteny
Align Sequences By Their Amino Acid Translation	AlignTranslation
Simulate Amplification of DNA by PCR	AmplifyDNA
Create a Matrix Representation of a Microarray	Array2Matrix
BLOSUM Amino Acid Substitution Matrices	BLOSUM
View a Database Table in a Web Browser	BrowseDB
View Sequences in a Web Browser	BrowseSeqs
Predict the Hybridization Efficiency of Probe/Target Sequence Pairs	CalculateEfficiencyArray
Predict Thermodynamic Parameters of Probe/Target Sequence Pairs	CalculateEfficiencyFISH
Predict Amplification Efficiency of Primer Sequences	CalculateEfficiencyPCR
Cluster Sequences By Distance	Clusterize
Compression/Decompression of Character Vectors	Codec
Create a Consensus Sequence	ConsensusSequence
Compute cophenetic distances on dendrogram objects	Cophenetic
Corrects Frameshift Errors In Protein Coding Sequences	CorrectFrameshifts
Create Artificial Chimeras	CreateChimeras
Export Database Sequences to a FASTA or FASTQ File	DB2Seqs
Free Energy of Hybridization of Probe/Target Quadruplets on Microarrays	deltaGrules
Pseudoenergy Parameters for RNA Quadruplets	deltaGrulesRNA
Change in Enthalpy of Hybridization of DNA/DNA Quadruplets in Solution	deltaHrules
Change in Enthalpy of Hybridization of RNA/RNA Quadruplets in Solution	deltaHrulesRNA
Change in Entropy of Hybridization of DNA/DNA Quadruplets in Solution	deltaSrules
Change in Entropy of Hybridization of RNA/RNA Quadruplets in Solution	deltaSrulesRNA
Design a Set of DNA Microarray Probes for Detecting Sequences	DesignArray
Design PCR Primers Targeting a Specific Group of Sequences	DesignPrimers
Design FISH Probes Targeting a Specific Group of Sequences	DesignProbes
Design PCR Primers for Amplifying Group-Specific Signatures	DesignSignatures
Detect Repeats in a Sequence	DetectRepeats
Simulate Restriction Digestion of DNA	DigestDNA
Expand Ambiguities into All Permutations of a DNAStringSet	Disambiguate
Calculate the Distances Between Sequences	DistanceMatrix
Extract Predicted Genes from a Genome	ExtractGenes
Find Chimeras in a Sequence Database	FindChimeras
Find Genes in a Genome	FindGenes
Find Non-Coding RNAs in a Genome	FindNonCoding
Finds Synteny in a Sequence Database	FindSynteny
Forms Groups By Rank	FormGroups
Genes objects and accessors	Genes-class plot.Genes print.Genes [.Genes
Mutual Information for Protein Secondary Structure Prediction	HEC_MI1 HEC_MI2
Create Consensus Sequences by Groups	IdConsensus
Identify By Taxonomic Rank	IdentifyByRank
Determine the Number of Characters in Each Sequence	IdLengths
Assign Sequences a Taxonomic Classification	IdTaxa
Build an inverted index	IndexSeqs
Fit Recombination Parameters to Correlation Profiles	InferRecombination
InvertedIndex objects	InvertedIndex-class print.InvertedIndex
Learn a Non-Coding RNA Model	LearnNonCoding
Train a Classifier for Assigning Taxonomy	LearnTaxa
Map Changes in Ancestral Character States	MapCharacters
Mask Highly Variable Regions of An Alignment	MaskAlignment
Simulate Melting of DNA	MeltDNA
MIQS Amino Acid Substitution Matrix	MIQS
MMLSUM Amino Acid Substitution Matrices	MMLSUM
Available Models of Sequence Evolution	MODELS
Sequential Coordinate-wise Algorithm for the Non-negative Least Squares Problem	NNLS
NonCoding Objects and Methods	NonCoding-class print.NonCoding
NonCoding Models for Common Non-Coding RNA Families	NonCodingRNA_Archaea NonCodingRNA_Bacteria NonCodingRNA_Eukarya
Orient Nucleotide Sequences	OrientNucleotides
PAM Amino Acid Substitution Matrices	PAM
PFASUM Amino Acid Substitution Matrices	PFASUM
Predict RNA Secondary Structure in Dot-Bracket Notation	PredictDBN
Predict Protein Secondary Structure	PredictHEC
Read a Dendrogram from a Newick Formatted File	ReadDendrogram
Remove Gap Characters in Sequences	RemoveGaps
Common Restriction Enzyme's Cut Sites	RESTRICTION_ENZYMES
Score a Multiple Sequence Alignment	ScoreAlignment
Obtain Specific Sequences from a Database	SearchDB
Search an inverted index	SearchIndex
Add Sequences from Text File to Database	Seqs2DB
Produce a Staggered Alignment	StaggerAlignment
Synteny blocks and hits	as.dist.Synteny pairs.Synteny plot.Synteny print.Synteny Synteny-class [.Synteny
Taxa training and testing objects	c.Taxa plot.Taxa print.Taxa Taxa-class [.Taxa
Determine the Number of Terminal Characters	TerminalChar
Form a Set of Tiles for Each Group of Sequences.	TileSeqs
Training Set for Classification of 16S rRNA Gene Sequences	TrainingSet_16S
Construct a Phylogenetic Tree	TreeLine Treeline
Trims DNA Sequences to the High Quality Region Between Patterns	TrimDNA
Write a Dendrogram to Newick Format	WriteDendrogram
Write Genes to a File	WriteGenes