DECIPHER

DOI: 10.18129/B9.bioc.DECIPHER    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DECIPHER.

Tools for curating, analyzing, and manipulating biological sequences

Bioconductor version: 3.15

A toolset for deciphering and managing biological sequences.

Author: Erik Wright

Maintainer: Erik Wright <eswright at pitt.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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		Reference Manual

Details

biocViews	Alignment, Clustering, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR
Version	2.24.0
In Bioconductor since	BioC 2.9 (R-2.14) (11 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
Suggests
SystemRequirements
Enhances
URL
Depends On Me	AssessORF, sangeranalyseR, SynExtend
Imports Me	AssessORFData, mia, openPrimeR
Suggests Me	MicrobiotaProcess
Links To Me
Build Report

Package Archives

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

Source Package	DECIPHER_2.24.0.tar.gz
Windows Binary	DECIPHER_2.24.0.zip
macOS Binary (x86_64)	DECIPHER_2.24.0.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