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This is the development version of DECIPHER; for the stable release version, see DECIPHER.

Tools for curating, analyzing, and manipulating biological sequences

Bioconductor version: Development (3.20)

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 "4.4") and enter:

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

# The following initializes usage of Bioc devel


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:

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
Searching biological sequences 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 R Script
Reference Manual PDF


biocViews Alignment, Clustering, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR
Version 3.1.4
In Bioconductor since BioC 2.9 (R-2.14) (12.5 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings(>= 2.59.1), stats
Imports methods, DBI, S4Vectors, IRanges, XVector
System Requirements
See More
Suggests RSQLite (>= 1.1)
Linking To Biostrings, S4Vectors, IRanges, XVector
Depends On Me AssessORF, sangeranalyseR, SynExtend
Imports Me mia, openPrimeR, scifer, copyseparator, ensembleTax
Suggests Me MicrobiotaProcess, microbial, MiscMetabar
Links To Me
Build Report Build Report

Package Archives

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

Source Package DECIPHER_3.1.4.tar.gz
Windows Binary
macOS Binary (x86_64) DECIPHER_3.1.4.tgz
macOS Binary (arm64) DECIPHER_3.1.4.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Package Short Url
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