DECIPHER
This is the development version of DECIPHER; for the stable release version, see DECIPHER.
Tools for curating, analyzing, and manipulating biological sequences
Bioconductor version: Development (3.24)
A toolset for deciphering and managing biological sequences.
Author: Erik Wright
Maintainer: Erik Wright <Erik.Wright at bcm.edu>
citation("DECIPHER")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | R Script | |
| Design Group-Specific FISH Probes in R | R Script | |
| Design Group-Specific Primers in R | R Script | |
| Design Microarray Probes in R | R Script | |
| Design Primers that Yield Group-Specific Signatures | R Script | |
| Detecting Obscure Tandem Repeats in Sequences | R Script | |
| Finding Chimeric Sequences in R | R Script | |
| Getting Started DECIPHERing | R Script | |
| Growing Phylogenetic Trees in R with Treeline | R Script | |
| Population Genetics Inference in R | R Script | |
| Searching Biological Sequences for Research | 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, Classification, Clustering, ComparativeGenomics, DataImport, GenePrediction, Genetics, ImmunoOncology, Microarray, Microbiome, Phylogenetics, QualityControl, SequenceMatching, Sequencing, Software, Visualization, WholeGenome, qPCR |
| Version | 3.9.2 |
| 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 |
See More
| 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, piglet, tidyGenR, 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_3.9.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | DECIPHER_3.9.2.tgz |
| macOS Binary (sonoma-arm64) | DECIPHER_3.9.2.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 |