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.
|Depends:||R (>= 2.13.0), Biostrings (>= 2.35.12), RSQLite (>= 1.1), stats, parallel|
|Imports:||methods, DBI, S4Vectors, IRanges, XVector|
|LinkingTo:||Biostrings, RSQLite, S4Vectors, IRanges, XVector|
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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 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 Primer/Target Quadruplets in Solution deltaSrules Change in Entropy of Hybridization of Primer/Target 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 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 Sequence IdTaxa Assign Sequences a Taxonomic Classification LearnTaxa Train a Classifier for Assigning Taxonomy 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
Maintainer: Erik Wright <[email protected]>
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