DECIPHER-package: Tools for curating, analyzing, and manipulating biological...
In DECIPHER: 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 (>= 2.35.12), RSQLite (>= 1.1), stats, parallel
Imports: methods, DBI, S4Vectors, IRanges, XVector
LinkingTo: Biostrings, RSQLite, S4Vectors, IRanges, XVector
License: GPL-3
LazyLoad: yes
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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
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
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
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
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>
DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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 (>= 2.35.12), RSQLite (>= 1.1), stats, parallel |
| Imports: | methods, DBI, S4Vectors, IRanges, XVector |
| LinkingTo: | Biostrings, RSQLite, S4Vectors, IRanges, XVector |
| License: | GPL-3 |
| LazyLoad: | yes |
Index:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 | 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
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
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
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
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>
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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