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DECIPHER

Tools for curating, analyzing, and manipulating biological sequences


Bioconductor version: Release (3.19)

A toolset for deciphering and managing biological sequences.

Author: Erik Wright

Maintainer: Erik Wright <eswright at pitt.edu>

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

Installation

To install this package, start R (version "4.4") 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")
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

Details

biocViews Alignment, Clustering, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR
Version 3.0.0
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
URL
See More
Suggests RSQLite (>= 1.1)
Linking To Biostrings, S4Vectors, IRanges, XVector
Enhances
Depends On Me AssessORF, sangeranalyseR, SynExtend
Imports Me mia, openPrimeR, scifer, AssessORFData, 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_3.0.0.tar.gz
Windows Binary DECIPHER_3.0.0.zip
macOS Binary (x86_64) DECIPHER_3.0.0.tgz
macOS Binary (arm64) DECIPHER_3.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/DECIPHER
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DECIPHER
Bioc Package Browser https://code.bioconductor.org/browse/DECIPHER/
Package Short Url https://bioconductor.org/packages/DECIPHER/
Package Downloads Report Download Stats