DECIPHER

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

Tools for curating, analyzing, and manipulating biological sequences

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DOI: 10.18129/B9.bioc.DECIPHER

Bioconductor version: Development (3.23)

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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 in R PDF R Script

Design Group-Specific FISH Probes in R PDF R Script

Design Group-Specific Primers in R PDF R Script

Design Microarray Probes in R 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 in R PDF R Script

Getting Started DECIPHERing PDF R Script

Growing Phylogenetic Trees in R with Treeline PDF R Script

Population Genetics Inference in R PDF R Script

Searching Biological Sequences for Research 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Clustering, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, QualityControl, Sequencing, Software, Visualization, WholeGenome, qPCR

Version 3.7.0

In Bioconductor since BioC 2.9 (R-2.14) (14 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 DspikeIn, mia, openPrimeR, scifer, AssessORFData, copyseparator, ensembleTax, VIProDesign

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_3.7.0.tar.gz

Windows Binary (x86_64) DECIPHER_3.7.0.zip (64-bit only)

macOS Binary (x86_64) DECIPHER_3.7.0.tgz

macOS Binary (arm64) DECIPHER_3.7.0.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/

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