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

A toolset for deciphering and managing biological sequences.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("DECIPHER")
AuthorErik Wright
Bioconductor views Alignment Clustering DataImport Genetics Microarray Microbiome QualityControl Sequencing Visualization WholeGenome qPCR
Date of publicationNone
MaintainerErik Wright <eswright@pitt.edu>
LicenseGPL-3
Version2.4.0

View on Bioconductor

Man pages

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...

CalculateEfficiencyFISH: Predict Thermodynamic Parameters of Probe/Target Sequence...

CalculateEfficiencyPCR: Predict Amplification Efficiency of Primer Sequences

Codec: Compression/Decompression of Character Vectors

ConsensusSequence: Create a Consensus Sequence

CorrectFrameshifts: Corrects Frameshift Errors In Protein Coding Sequences

CreateChimeras: Create Artificial Chimeras

DB2Seqs: Export Database Sequences to a FASTA or FASTQ File

DECIPHER-package: Tools for curating, analyzing, and manipulating biological...

deltaGrules: Free Energy of Hybridization of Probe/Target Quadruplets on...

deltaHrules: Change in Enthalpy of Hybridization of Primer/Target...

deltaSrules: Change in Entropy of Hybridization of Primer/Target...

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

DigestDNA: Simulate Restriction Digestion of DNA

Disambiguate: Expand Ambiguities into All Permutations of a DNAStringSet

DistanceMatrix: Calculate the Distances Between Sequences

FindChimeras: Find Chimeras in a Sequence Database

FindSynteny: Finds Synteny in a Sequence Database

FormGroups: Forms Groups By Rank

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...

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...

OrientNucleotides: Orient Nucleotide Sequences

PredictDBN: Predict RNA Secondary Structure in Dot-Bracket Notation

PredictHEC: Predict Protein Secondary Structure as Helix, Beta-Sheet, or...

ReadDendrogram: Read a Dendrogram from a Newick Formatted File

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

TerminalChar: Determine the Number of Terminal Characters

TileSeqs: Form a Set of Tiles for Each Group of Sequences.

TrimDNA: Trims DNA Sequences to the High Quality Region Between...

WriteDendrogram: Write a Dendrogram to Newick Format

Functions

Add2DB Man page
AdjustAlignment Man page
AlignDB Man page
AlignProfiles Man page
AlignSeqs Man page
AlignSynteny Man page
AlignTranslation Man page
AmplifyDNA Man page
Array2Matrix Man page
BrowseDB Man page
BrowseSeqs Man page
CalculateEfficiencyArray Man page
CalculateEfficiencyFISH Man page
CalculateEfficiencyPCR Man page
Codec Man page
ConsensusSequence Man page
CorrectFrameshifts Man page
CreateChimeras Man page
DB2Seqs Man page
DECIPHER Man page
DECIPHER-package Man page
deltaGrules Man page
deltaHrules Man page
deltaSrules Man page
DesignArray Man page
DesignPrimers Man page
DesignProbes Man page
DesignSignatures Man page
DigestDNA Man page
Disambiguate Man page
DistanceMatrix Man page
FindChimeras Man page
FindSynteny Man page
FormGroups Man page
HEC_MI1 Man page
HEC_MI2 Man page
IdClusters Man page
IdConsensus Man page
IdentifyByRank Man page
IdLengths Man page
MaskAlignment Man page
MeltDNA Man page
MIQS Man page
MODELS Man page
NNLS Man page
OrientNucleotides Man page
pairs.Synteny Man page
plot.Synteny Man page
PredictDBN Man page
PredictHEC Man page
print.Synteny Man page
ReadDendrogram Man page
RESTRICTION_ENZYMES Man page
SearchDB Man page
Seqs2DB Man page
StaggerAlignment Man page
[.Synteny Man page
Synteny-class Man page
TerminalChar Man page
TileSeqs Man page
TrimDNA Man page
WriteDendrogram Man page

Files

DESCRIPTION
NAMESPACE
R
R/Add2DB.R R/AdjustAlignment.R R/AlignDB.R R/AlignProfiles.R R/AlignSeqs.R R/AlignSynteny.R R/AlignTranslation.R R/AmplifyDNA.R R/Array2Matrix.R R/BrowseDB.R R/BrowseSeqs.R R/CalculateEfficiencyArray.R R/CalculateEfficiencyFISH.R R/CalculateEfficiencyPCR.R R/Codec.R R/ConsensusSequence.R R/CorrectFrameshifts.R R/CreateChimeras.R R/DB2Seqs.R R/DesignArray.R R/DesignPrimers.R R/DesignProbes.R R/DesignSignatures.R R/DigestDNA.R R/Disambiguate.R R/DistanceMatrix.R R/FindChimeras.R R/FindSynteny.R R/FormGroups.R R/IdClusters.R R/IdConsensus.R R/IdLengths.R R/IdentifyByRank.R R/MaskAlignment.R R/MeltDNA.R R/NNLS.R R/OrientNucleotides.R R/PredictDBN.R R/PredictHEC.R R/ReadDendrogram.R R/SearchDB.R R/Seqs2DB.R R/StaggerAlignment.R R/Synteny-class.R R/TerminalChar.R R/TileSeqs.R R/TrimDNA.R R/WriteDendrogram.R R/utils.R R/zzz.R
build
build/vignette.rds
data
data/HEC_MI1.RData
data/HEC_MI2.RData
data/MIQS.RData
data/RESTRICTION_ENZYMES.RData
data/datalist
data/deltaGrules.RData
data/deltaHrules.RData
data/deltaSrules.RData
inst
inst/CITATION
inst/doc
inst/doc/ArtOfAlignmentInR.R
inst/doc/ArtOfAlignmentInR.Rnw
inst/doc/ArtOfAlignmentInR.pdf
inst/doc/DECIPHERing.R
inst/doc/DECIPHERing.Rnw
inst/doc/DECIPHERing.pdf
inst/doc/DesignMicroarray.R
inst/doc/DesignMicroarray.Rnw
inst/doc/DesignMicroarray.pdf
inst/doc/DesignPrimers.R
inst/doc/DesignPrimers.Rnw
inst/doc/DesignPrimers.pdf
inst/doc/DesignProbes.R
inst/doc/DesignProbes.Rnw
inst/doc/DesignProbes.pdf
inst/doc/DesignSignatures.R
inst/doc/DesignSignatures.Rnw
inst/doc/DesignSignatures.pdf
inst/doc/FindChimeras.R
inst/doc/FindChimeras.Rnw
inst/doc/FindChimeras.pdf
inst/extdata
inst/extdata/50S_ribosomal_protein_L2.fas
inst/extdata/Bacteria_175seqs.fas
inst/extdata/Bacteria_175seqs.gen
inst/extdata/Bacteria_175seqs.sqlite
inst/extdata/IDH2.fas
inst/extdata/Influenza.sqlite
inst/extdata/Streptomyces_ITS_aligned.fas
man
man/Add2DB.Rd man/AdjustAlignment.Rd man/AlignDB.Rd man/AlignProfiles.Rd man/AlignSeqs.Rd man/AlignSynteny.Rd man/AlignTranslation.Rd man/AmplifyDNA.Rd man/Array2Matrix.Rd man/BrowseDB.Rd man/BrowseSeqs.Rd man/CalculateEfficiencyArray.Rd man/CalculateEfficiencyFISH.Rd man/CalculateEfficiencyPCR.Rd man/Codec.Rd man/ConsensusSequence.Rd man/CorrectFrameshifts.Rd man/CreateChimeras.Rd man/DB2Seqs.Rd man/DECIPHER-package.Rd man/DesignArray.Rd man/DesignPrimers.Rd man/DesignProbes.Rd man/DesignSignatures.Rd man/DigestDNA.Rd man/Disambiguate.Rd man/DistanceMatrix.Rd man/FindChimeras.Rd man/FindSynteny.Rd man/FormGroups.Rd man/HEC_MI.Rd man/IdClusters.Rd man/IdConsensus.Rd man/IdLengths.Rd man/IdentifyByRank.Rd man/MIQS.Rd man/MODELS.Rd man/MaskAlignment.Rd man/MeltDNA.Rd man/NNLS.Rd man/OrientNucleotides.Rd man/PredictDBN.Rd man/PredictHEC.Rd man/RESTRICTION_ENZYMES.Rd man/ReadDendrogram.Rd man/SearchDB.Rd man/Seqs2DB.Rd man/StaggerAlignment.Rd man/Synteny-class.Rd man/TerminalChar.Rd man/TileSeqs.Rd man/TrimDNA.Rd man/WriteDendrogram.Rd man/deltaGrules.Rd man/deltaHrules.Rd man/deltaSrules.Rd
src
src/AlignProfiles.c
src/AssignIndels.c
src/Biostrings_stubs.c
src/CalculateDeltaG.c
src/CalculateFISH.c
src/ChainSegments.c
src/ClusterML.c
src/ClusterNJ.c
src/ClusterUPGMA.c
src/CommonGaps.c
src/Compositions.c
src/Compression.c
src/ConsensusSequence.c
src/ConsolidateGaps.c
src/DECIPHER.h
src/DesignProbes.c
src/Diff.c
src/DistanceMatrix.c
src/EnumerateSequence.c
src/ExpandAmbiguities.c
src/FindFrameshifts.c
src/GetPools.c
src/Import.c
src/InformationContent.c
src/InsertGaps.c
src/IntDist.c
src/Makevars
src/MeltPolymer.c
src/MovingAverage.c
src/MultiMatch.c
src/NNLS.c
src/Order.c
src/PredictDBN.c
src/PredictHEC.c
src/R_init_decipher.c
src/RemoveGaps.c
src/ReplaceChars.c
src/TerminalMismatch.c
src/Translate.c
src/XVector_stubs.c
vignettes
vignettes/AlignmentBenchmarks.pdf
vignettes/AlignmentFlowChart.pdf
vignettes/AlignmentSpace1.png
vignettes/AlignmentSpace2.png
vignettes/AmpliconSignatures.pdf
vignettes/ArtOfAlignmentInR.Rnw
vignettes/BrowseAmpliconOutput.png
vignettes/BrowseDBOutput.png
vignettes/BrowseProbesOutput.png
vignettes/BrowseSeqsOutput.png
vignettes/BrowseSignaturesOutput.png
vignettes/DECIPHERing.Rnw
vignettes/DefaultVsChainedGuideTrees.pdf
vignettes/DenaturationPlot.pdf
vignettes/DesignMicroarray.Rnw
vignettes/DesignPrimers.Rnw
vignettes/DesignProbes.Rnw
vignettes/DesignSignatures.Rnw
vignettes/DigestedSignatures.pdf
vignettes/DualProbesScores.png
vignettes/FindChimeras.Rnw
vignettes/FormamideCurve.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.