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

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A toolset for deciphering and managing biological sequences.

Author
Erik Wright
Date of publication
None
Maintainer
Erik Wright <DECIPHER@cae.wisc.edu>
License
GPL-3
Version
2.2.0

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

Files in this package

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