DECIPHER

This is the released version of DECIPHER; for the devel version, see DECIPHER.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9

Tools for curating, analyzing, and manipulating biological sequences

Bioconductor version: Release (3.23)

A toolset for deciphering and managing biological sequences.

Author: Erik Wright

Maintainer: Erik Wright <Erik.Wright at bcm.edu>

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

Erik Wright. DECIPHER: Tools for curating, analyzing, and manipulating biological sequences. doi:10.18129/B9.bioc.DECIPHER, R package version 3.8.1, https://bioconductor.org/packages/DECIPHER.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DECIPHER")

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

Documentation

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

browseVignettes("DECIPHER")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Clustering, ComparativeGenomics, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, Phylogenetics, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR
Version	3.8.1
In Bioconductor since	BioC 2.9 (R-2.14) (15 years)
License	GPL-3
Depends	R (>= 3.5.0), Biostrings (>= 2.59.1), stats
Imports	methods, DBI, S4Vectors, IRanges, XVector
System Requirements
URL	http://DECIPHER.codes

Suggests	RSQLite (>= 1.1)
Linking To	Biostrings, S4Vectors, IRanges, XVector
Enhances
Depends On Me	AssessORF, sangeranalyseR, SynExtend
Imports Me	AssessORFData, copyseparator, DspikeIn, ensembleTax, mia, openPrimeR, piglet, scifer, tidyGenR, VIProDesign
Suggests Me	microbial, MicrobiotaProcess, MiscMetabar
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	DECIPHER_3.8.1.tar.gz
Windows Binary (x86_64)	DECIPHER_3.8.1.zip (64-bit only)
macOS Binary (big-sur-x86_64)	DECIPHER_3.8.1.tgz
macOS Binary (sonoma-arm64)	DECIPHER_3.8.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DECIPHER
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DECIPHER
Package Short Url	https://bioconductor.org/packages/DECIPHER/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.23	Source Archive