DECIPHER
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see DECIPHER.
Tools for curating, analyzing, and manipulating biological sequences
Bioconductor version: 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 | R Script | |
| Design Group-Specific FISH Probes | R Script | |
| Design Group-Specific Primers | R Script | |
| Design Microarray Probes | R Script | |
| Design Primers That Yield Group-Specific Signatures | R Script | |
| Detecting Obscure Tandem Repeats in Sequences | R Script | |
| Finding Chimeric Sequences | R Script | |
| Getting Started DECIPHERing | R Script | |
| Growing Phylogenetic Trees with TreeLine | R Script | |
| Searching biological sequences | R Script | |
| The Art of Multiple Sequence Alignment in R | R Script | |
| The Double Life of RNA: Uncovering Non-Coding RNAs | R Script | |
| The Magic of Gene Finding | R Script | |
| Upsize Your Clustering with Clusterize | R Script | |
| Reference Manual |
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) (13 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, SynExtend, sangeranalyseR |
| 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 (x86_64) | 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 |