DOI: 10.18129/B9.bioc.DECIPHER  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see DECIPHER.

Tools for curating, analyzing, and manipulating biological sequences

Bioconductor version: 3.17

A toolset for deciphering and managing biological sequences.

Author: Erik Wright

Maintainer: Erik Wright <eswright at>

Citation (from within R, enter citation("DECIPHER")):


To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:



PDF R Script Classify Sequences
PDF R Script Design Group-Specific FISH Probes
PDF R Script Design Group-Specific Primers
PDF R Script Design Microarray Probes
PDF R Script Design Primers That Yield Group-Specific Signatures
PDF R Script Detecting Obscure Tandem Repeats in Sequences
PDF R Script Finding Chimeric Sequences
PDF R Script Getting Started DECIPHERing
PDF R Script Growing Phylogenetic Trees with TreeLine
PDF R Script The Art of Multiple Sequence Alignment in R
PDF R Script The Double Life of RNA: Uncovering Non-Coding RNAs
PDF R Script The Magic of Gene Finding
PDF R Script Upsize Your Clustering with Clusterize
PDF   Reference Manual


biocViews Alignment, Clustering, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR
Version 2.28.0
In Bioconductor since BioC 2.9 (R-2.14) (12 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings(>= 2.59.1), RSQLite (>= 1.1), stats, parallel
Imports methods, DBI, S4Vectors, IRanges, XVector
LinkingTo Biostrings, S4Vectors, IRanges, XVector
Depends On Me AssessORF, sangeranalyseR, SynExtend
Imports Me AssessORFData, mia, openPrimeR, scifer
Suggests Me MicrobiotaProcess
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package DECIPHER_2.28.0.tar.gz
Windows Binary
macOS Binary (x86_64) DECIPHER_2.28.0.tgz
macOS Binary (arm64) DECIPHER_2.28.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats

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